Chapter 1

Biodiversity

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 CHAPTER 1: BIODIVERSITY

1.1 Biodiversity And Classification

1.2 Domain Bacteria And Domain Archaea
1.4 Domain Eukarya: Kingdom Protista
1.5 Domain Eukarya: Kingdom Fungi
1.6 Domain Eukarya: Kingdom Plantae
1.7 Domain Eukarya: Kingdom Animalia
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 1. 1
BIODIVERSITY AND CLASSIFICATION

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 1. 1 BIODIVERSITY AND CLASSIFICATION

OBJECTIVES:

a) C1 : State types of biodiversity (genetic, species and

ecosystem).

a) C1 : State hierarchical classification

a) C3 : Explain briefly the three-domain system (Carl

Woese,1977) - Bacteria, Archaea and Eukarya based
on rRNA base sequence.
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a) State types of biodiversity (genetic, species and ecosystem).

Biodiversity
• Bio means life or living organisms.

• Diversity means variety or differences of individuals

in a group.

• Biodiversity or biological diversity is defined as the

variety of life on Earth at all its level, from gene to
ecosystem.

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 3 TYPES OF BIODIVERSITY:
• Genetic diversity : The genetic variability
within a species

• Species diversity : The variety of species

within a community

• Ecosystem diversity : Distribution and

abundance of living organisms and the
interactions among them & their environment
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 Genetic diversity
• The combination of different genes found
within a population of a single species or
within different populations of the same
species.

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 Species diversity
• The variety of species in an ecosystem or
throughout the entire biosphere

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 Ecosystem diversity
• The variety of ecosystems and ecological
processes in the biosphere as well as the
diversity within ecosystems.

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b) State hierarchical classification

HIERARCHICAL CLASSIFICATION

• A hierarchical system is used for classifying

organisms to the species level.

• This system is called taxonomic classification.

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• In naming species, Linnaean System groups
organisms into hierarchy of increasingly
inclusive categories (taxonomic system)

• The named taxonomic unit at any level of the

hierarchy is called a taxon (pl. taxa)

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 TAXONOMY
• Definition :
– The science of naming, describing and classifying
organisms.

• It includes
- Identification
- Classification
- Nomenclature (naming)

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TAXONOMY
• Biological classification is
based on taxon
• Taxon : A group of organism at
a particular level in a
classification system.
• In Taxonomy Hierarchy, there
are 8 taxa
• The broadest classifications are
by domain while the most
specific classification is by
species.
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 ● Species that appear to be closely
related are grouped into the same
genus.
● Closely related genera are placed
into a family.
● Closely related families are grouped
into an order.
● Closely related orders are grouped
into a class.
● Closely related classes are grouped
into a phylum.
● Closely related phyla are grouped
into a kingdom.
● Kingdoms are grouped into a
*own drawing
domain.
(*) closely related means having the most similarities or common characteristics
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 EXAMPLE
Domain : Eukarya
Kingdom : Animalia
Phylum : Chordata
Class : Mammalia
Order : Carnivora
Family : Felidae
Genus : Panthera
Species : Panthera pardus

Scientific name handwritten :

Panthera pardus or
P. pardus
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 EXAMPLE
Domain : Eukarya
Kingdom : Plantae
Phylum : Magnoliophyta
Class : Magnoliopsida
Order : Malvales
Family : Malvaceae
Genus : Durio
Species : Durio zibethinus

Scientific name handwritten :

Durio zibethinus or
D. zibethinus
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 EXAMPLE
Domain : Bacteria
Kingdom : Monera
Phylum : Proteobacteria
Class : Gammaproteobacteria
Order : Enterobacteriales
Family : Enterobacteriaceae
Genus : Escherichia
Species : Escherichia coli

Scientific name handwritten :

Escherichia coli or
E. coli
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According to taxonomy, Coyote & Gray Wolf are classified under same Domain, Kingdom,
Phylum, Class, Order, Family & Genus, but different Species.

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 BINOMIAL NOMENCLATURE

• Binomial nomenclature (two-name naming system) is

the naming system of an organism

• Scientific name composed of two parts which are Genus and

Species. Both of which usually use Latin language:
- The first part is the Genus (generic name)
- The second part is the Species (specific name).

• Introduced by Swedish naturalist Carl Linnaeus.

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 BINOMIAL NOMENCLATURE

• The first alphabet of the Genus is written in capital letter.

• All letters in the species are lowercases.

• Both parts are italicized (if typed) or underlined (if

handwritten)

• Example :
Common name: Frog
Scientific name: Rana temporaria (If typed)
Rana temporaria (If handwritten)
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 ANOTHER FORMAT TO WRITE SCIENTIFIC
NAME
• If Genus of an organism is known but its Species is
unknown, its scientific name can be written as:
− Sulfolobus sp. or Sulfolobus sp.

• Genus : Sulfolobus or Sulfolobus

– First letter is capitalized, italicized if typed or
underlined if handwritten

• Species : sp.
– all lowercase, ended with dot, not italicized or
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c) Explain briefly the three-domain system (Carl Woese,1977)

THREE DOMAIN SYSTEM

• Three-domain system introduced by Carl Woese
(1977)
• In three-domain system, organisms are classified
based on the ribosomal RNA (rRNA) base sequence
• rRNA – molecular building block for ribosomes.
• 3 domains:
(i) Domain Bacteria
(ii) Domain Archaea
(iii) Domain Eukarya

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 THREE DOMAIN SYSTEM
• Domain Bacteria and Archaea
– Prokaryotes
– Mostly single cell and microscopic

• Domain Eukarya
– Eukaryotes
– Include both unicellular and multicellular
organisms
• Unicellular: Kingdom Protista
• Multicellular: Kingdom Protista, Kingdom Fungi,
Kingdom Plantae and Kingdom Animalia
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 1. 2
DOMAIN BACTERIA AND ARCHAEA

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 1. 2 DOMAIN BACTERIA AND ARCHAEA

Objectives:
1. C1 : State the two domains of prokaryotes, Bacteria (E. coli)
and Archaea (Sulfolobus sp.)
2. C2 : Differentiate between the two domains of prokaryotes,
Bacteria (E. coli) and Archaea (Sulfolobus sp.) based on :
– Cell wall structure
– Association of histone to DNA
– Structure of membrane lipids
3. C2 : Describe the diversity of bacteria based on
– cell shapes
– Gram-stain
4. C3 : Explain the role of bacteria
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1)State the two domains of prokaryotes, Bacteria (E. coli) and Archaea (Sulfolobus sp.)

CLASSIFICATION OF PROKARYOTES

Prokaryotes can be classified into two Domains

1. Domain Bacteria
▪ Escherichia coli
▪ Cyanobacteria (blue green algae)

2. Domain Archaea
▪ e.g. Sulfolobus sp.

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 Domain Bacteria
• True bacteria
• Unicellular prokaryote
• Most are adaptable to diverse environment
• Cell wall : made of peptidoglycan
• Membrane lipid : has unbranched
hydrocarbon chain attached to ester linkage
• DNA : not associate with histone protein
• Example : E. coli

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E.coli (Escherichia coli)

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Bacterial cell wall
lipopolysaccharide

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 Domain Archaea
• Ancient bacteria
• lives in extreme environment
• Unicellular prokaryote
• Cell wall: absence of peptidoglycan
• Structure of membrane lipid: has branched
hydrocarbon chain linked to glycerol by ether
linkage
• DNA: associates with histone protein
• Example : Sulfolobus sp.
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 2) Differentiate between the two domains of prokaryotes, Bacteria (E. coli) and Archaea (Sulfolobus sp.)
DIFFERENCES BETWEEN DOMAIN BACTERIA AND
DOMAIN ARCHAEA

BACTERIA ARCHAEA
Cell wall contain peptidoglycan Cell wall lack of peptidoglycan

In plasma membrane, In plasma membrane, branched

unbranched hydrocarbon chain hydrocarbon chain are linked to
are linked to glycerol by ester glycerol by ether linkage
linkage

DNA is not associated with DNA is associated with histone

histone

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 COMPARISON BETWEEN DOMAIN BACTERIA AND DOMAIN ARCHAEA

Characteristic Domain Bacteria Domain Archaea

Nuclear envelope DNA can be found in the nucleoid region

Membrane bounded Absent

organelle
Component of cell wall Made up of peptidoglycan Made up of pseudopeptidoglycan
Absent of peptidoglycan

Membrane lipids Has unbranched Has branched hydrocarbons

hydrocarbons/Hydrocarbon Hydrocarbon chain link to glycerol
chain link to glycerol by ester by ether linkage
linkage
Association of Histone Absent Present
to DNA
Structure of Circular
Chromosome/DNA
Plasmid Present
Ribosome size 70S

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3) Describe the diversity of bacteria based on; cell shapes & Gram-stain

DIVERSITY OF BACTERIA

• Varies type of bacteria found in varies area on Earth

• Bacteria can be classified based on :

i. Cell shapes
− Coccus, Bacillus, Spirillum & Vibrio

ii. Gram-stain
− Gram positive & Gram negative

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 COCCUS
▪ Plural : cocci
▪ Spherical shape
▪ Unicellular, two-celled or colonies (chain, cluster)
▪ Example:

Two celled : diplococcus Chain : streptococcus Clump: staphylococcus

E.g: Neisseria sp. E.g: Streptococcus sp. E.g: Staphylococcus sp.

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 BACILLUS
▪ Plural : bacilli

▪ Rod shape

▪ Unicellular, colonies
(chain)

▪ E.g. Bacillus
thuringiensis, E. coli

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 SPIRILLUM
▪ Plural : spirilla

▪ Spiral shape

▪ Unicellular

▪ E.g. Rhodospirillum sp.

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 VIBRIO
▪ Known as vibrio

▪ Comma shape

▪ Unicellular

▪ E.g. Vibrio cholerae

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 DIVERSITY OF BACTERIA : GRAM STAIN

Gram stain

Gram-positive Gram-negative
Lactobacillus sp. E. coli
Clostridium sp. Azotobacter sp.
Staphylococcus sp. Salmonella sp.

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 GRAM-POSITIVE BACTERIA
▪ Have simpler cell wall
▪ Thick peptidoglycan layer
▪ Stained blue or purple –stain trapped in the
peptidoglycan
▪ Less pathogenic and can be killed by antibiotic
(e.g Penicillin)
▪ Example : Bacillus sp. Clostridium sp.

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 GRAM-NEGATIVE BACTERIA
▪ Have more complex cell wall
▪ Thin peptidoglycan layer
▪ Lipopolysaccharide in outer membrane of the cell wall
▪ This lipopolysaccharides can be toxic
• The outer membrane protects them from the host’s defense,
i.e. can block entry of antibiotics
• Stained pink – blue dye washed out
• More pathogenic, cause diseases like typhoid, gonorrhea
• Example : Salmonella sp.
E. coli
Azotobacter sp.

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 Thick peptidoglycan Thin peptidoglycan
layer in cell wall to layer in cell wall hence cannot
retain crystal violet retain crystal violet stain but
stain even after retain the counterstain which is
decolorized by alcohol. safranin.

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 COMPARISON BETWEEN GRAM POSITIVE AND GRAM
NEGATIVE BACTERIA

Gram positive bacteria Gram negative bacteria

Cell wall has 1 layer which is thick
peptidoglycans layer
When stain with crystal violet dye,
cells will retain purple colour
Cell wall has 2 layer which are thin
peptidoglycans layer and outer
membrane layer
When stain with crystal violet and
safranin dye , cells does not retain
purple colour thus shows pink colour.

Less pathogenic // Can be killed by More pathogenic // Cannot be killed

antibiotic by antibiotic
Both have peptidoglycan.
Both are unicellular.

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4) Explain the role of bacteria

THE ROLE OF BACTERIA

I. Recycling of chemical elements in ecosystem (nitrogen
fixation)

• Atmospheric N2 must be reduced to NH3 by a process

known as nitrogen fixation
• The reaction is driven by the enzyme complex nitrogenase
that only found in prokaryote
• All nitrogen-fixing organisms are bacteria
• Among this group, Rhizobium sp. form efficient and
intimate associations with the roots of legumes

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2023, BYJU'S.

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 THE ROLE OF BACTERIA

II. Symbiotic (enterobacteria in human intestine , e.g E. coli)

• Symbiosis between microbes and their human host is vital to

maintain homeostasis
• Enterobacteria use human intestine as a shelter and provide an
array of benefits to the host, including promotion of host
immunity
• E. coli strain is a harmless enterobacteria which play an essential
role in keeping human digestive system healthy
• E. coli helps to digest lactose into glucose and galactose which is
used by human as respiratory substrate

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Credit KATERYNA KON / SCIENCE PHOTO LIBRARY

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 THE ROLE OF BACTERIA
III. Pathogenic
1. Salmonella : causing Salmonella
gastroenteritis (diarrhea, abdominal
cramps, and fever)
2. Clostridium tetani : causing tetanus
3. Vibrio cholerae : causing cholera
4. Treponema pallidum : causing syphilis

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https://my.clevelandclinic.org/health/diseases/15697-salmonella

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Credit KATERYNA KON / SCIENCE PHOTO LIBRARY

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 THE ROLE OF BACTERIA
IV. In research and technology

• Food technology - different species of bacteria used in the

making of cheeses, yoghurt and vinegar.

• In biotechnology such as in gene cloning, DNA plasmids from

bacteria are used as cloning vectors and the bacteria itself act
as the host cells.

• Product of biotechnology like Genetically Engineered - used to

produce vast quantities of human insulin and antibiotic to be
applied in pharmaceutical and medical field.

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