CHAPTER 1 BIODIVERSITY 1
1.0 Biodiversity 1.1 Biodiversity and Classification 1.2 Domain Bacteria and Archaea 1.3 Domain Eukarya: Kingdom Protista/Protoctista 1.4 Domain Eukarya: Kingdom Fungi 2
Learning outcomes : 1.1 Biodiversity and Classification (a) State types of biodiversity (genetic, species and ecosystem). (b) State hierarchical classification. (c) Explain briefly the three-domain system (Carl Woese, 1977) – Bacteria, Archaea and Eukarya based on rRNA base sequence. 3
Introduction of 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 all living organisms on Earth; living things in all forms and combinations’. Learning Outcomes : 1.1(a) State types of biodiversity (genetic, species and ecosystem) 4
Types of Biodiversity Learning Outcomes : 1.1(a) State types of biodiversity (genetic, species and ecosystem) ❖ Genetic diversity ❖ Species diversity ❖ Ecosystem diversity https://www.mrgscience.com/ess-topic-31-introduction-to-biodiversity.html 5
https://www.slideserve.com/ nitsa/chapter-14-mendeland-the-gene-idea i) Genetic diversity: • the variation of gene combinations among living organisms in a population of one species, and • between populations of the same species • to provide mechanism/specific phenotypes to adapt to environment. Learning Outcomes : 1.1(a) State types of biodiversity (genetic, species and ecosystem) Types of Biodiversity https://www.trufarm.org/store/25-lb-case-of-Organic-CherryBumblebee-Tomatoes-per-Case-p200678884 6
Learning Outcomes : 1.1(a) State types of biodiversity (genetic, species and ecosystem) ii) Species diversity: ❖ The rich variety of species (plants, animals and other life forms) within a region or ecosystem throughout the entire biosphere. https://biologyfreshwaterpje.weebly.com/pyramid.html 7
iii) Ecosystem diversity: ❖ The variety of habitats, biotic communities, ecological process within an ecosystem and the diversity of ecosystems in the biosphere. Learning Outcomes : 1.1(a) State types of biodiversity (genetic, species and ecosystem) http://www.eco-pros.org/images/Ecosystems/cactus2-5-1-0.jpg http://www.eco-pros.org/images/Ecosystems/forestfloorlife.jpg https://www.dandc.eu/en/article/cooperation-kfw-caribbean-biodiversity-fundsupports-marine-conservation-zones 8
• 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) Hierarchical Classification Learning Outcomes : 1.1(b) State hierarchical classification • species • genus (pl.genera) • family • order • class • phylum (pl. phyla) • kingdom • domain Increasingly inclusive 9
● 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 domain. (*) closely related means having the most similarities or common characteristics *own drawing
Learning Outcomes : 1.1(b) State hierarchical classification e.g. Species: Panthera pardus (leopard) Genus: Panthera (African lion, tiger, leopard) Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Domain: Eukarya http://tolweb.org/Panthera_pardus/123568 11
Learning Outcomes : 1.1(b) State hierarchical classification e.g. Species: Durio zibethinus (common durian) Genus: Durio (common durian, durian paya, durian merah) Family: Malvaceae Order: Malvales Class: Magnoliopsida Phylum: Magnoliophyta Kingdom: Plantae Domain: Eukarya https://www.thespruceeats.com/what-is-durian-4772269 12
Learning Outcomes : 1.1(c) Explain briefly the three-domain system Woese’s Three-Domain Classification System ❖ Bases of classification ■ The differences in ribosomal RNA (rRNA) nucleotide sequences, ■ among prokaryotes (K. Monera), archaea are separated from bacteria. ■ Kingdoms of eukaryotes classified under other domain. ❖ The three domains: ■Domain Bacteria ■Domain Archaea ■Domain Eukarya: (K. Protista, K. Plantae, K. Fungi, K. Animalia) 13
Learning Outcomes : 1.1(c) Explain briefly the three-domain system Woese’s Three-Domain Classification System http://fig.cox.miami.edu/~cmallery/150/scimeth/luca.htm 14
1.0 Biodiversity 1.1 Biodiversity and Classification 1.2 Domain Bacteria and Domain Archaea 1.3 Domain Eukarya: Kingdom Protista/Protoctista 1.4 Domain Eukarya: Kingdom Fungi 15
Learning outcomes : 1.2 Domains Bacteria and Archaea (a) State the two domains of prokaryotes (Bacteria and Archaea). (b) Differentiate between domains Bacteria and Archaea based on: (i) cell wall structure (ii) association of histone to DNA (iii) structure of membrane lipids (c) Describe the diversity of bacteria based on cell shapes and Gram stain. 16
Learning Outcomes : 1.2(a) State the two domains of prokaryotes, Bacteria and Archaea Prokaryote: General Structure https://www.thoughtco.com/prokaryotes-meaning-373369 17
CLASSIFICATION OF PROKARYOTES Domain Bacteria e.g. E. coli Domain Archaea e.g. Sulfolobus sp. Learning Outcomes : 1.2(a) State the two domain of prokaryotes,Bacteria and Archaea https://mrleehamber119.wordpress.com/2020/02/20/ch-2- images/archaebacteria-sulfolobus-hot-springs/ LECTURE Learning Outcomes : 1.2(a) State the two domains of prokaryotes, Bacteria and Archaea. LECTURE https://www.independent.co.uk/life-style/health-and-families/e-colibacteria-symptoms-infection-egypt-outbreak-treatment-explaineda8525486.html 18
(i) Domain Bacteria • True bacteria • Unicellular prokaryote • Most are adaptable to diverse environment • Cell wall: peptidoglycan • Structure of membrane lipid: unbranched hydrocarbon chain attached to ester linkage • DNA: without histone protein • e.g. E. coli E. coli Learning Outcomes : 1.2(a) State the two domains of prokaryotes, Bacteria and Archaea. State the two domain of prokaryotes,Bacteria and Archaea https://expathealth.org/health-advice/e-coli-health-information/ 19
ii) Domain Archaea • Unicellular prokaryote • Cell wall: absence of peptidoglycan • Structure of membrane lipid: branched hydrocarbon chain linked to glycerol by ether linkage • DNA: associates with histone protein • ancient bacteria • lives in extreme environment • e.g. Sulfolobus sp. Learning Outcomes : 1.2(a) State the two domain of prokaryotes,Bacteria and Archaea TUTORIAL 1.2(a) State the two domains of prokaryotes, Bacteria and Archaea. Sulfolobus solfataricus https://joidesresolution.org/microbe-monday-sulfolobus-solfataricus/ 20
Differences between Archaea & Bacteria Characteristics Archaea Bacteria Cell wall Peptidoglycan is absent Peptidoglycan is present Membrane lipid (i) Branched hydrocarbon chain Unbranched hydrocarbon chain Membrane lipid (ii) Ether linkage between glycerol and hydrocarbon chain Ester linkage between glycerol and hydrocarbon chain DNA Associates with histone protein Does not associate with histone protein Learning Outcomes : 1.2(b) Differentiate between the two domains of prokaryotes, Bacteria and Archaea based on cell wall structure, association of histone to DNA and structure of membrane lipids 21
Diversity of Bacteria Based on: (b) Gram stain Learning Outcomes : 1.2(c) Describe the diversity of bacteria (based on cell shapes and Gram stain (a) Cell shapes coccus bacillus spirillum https://www.thoughtco.com/bacteria-shapes-373278 https://www.aatbio.com/resources/faq-frequently-askedquestions/What-is-Gram-staining 22
(a) Cell shapes – Coccus: a spherical shape (pl. cocci); e.g. Staphylococcus sp. – Bacillus: a rod shape (pl. bacilli); e.g. E. coli – Spiral: cell body with one or more curves/twists; • spirillum (pl. spirilla), e.g. Rhodospirillum sp. • vibrio, e.g. Vibrio cholerae • spirochaete, e.g. Treponema pallidum Learning Outcomes : 1.2(c) Describe the diversity of bacteria (based on cell shapes and Gram stain https://www.topperlearning.com/frank-solutions/icse-class-9-biology/frankcertificate-biology-part-i/bacteria-and-fungi-their-importance 23
(b) Gram Stain Procedures for identifying bacteria based on the differences in their cell wall. Learning Outcomes : 1.2(c) Describe the diversity of bacteria (based on cell shapes and Gram stain https://www.globalindoorhealthnetwork.com/gram-stain 24
(b) Gram Stain (i) Gram-positive bacteria • Simple cell walls with thick peptidoglycan • Stained blue or purple, as peptidoglycan traps the crystal violet. • Less threatening pathogens • e.g. Clostridium sp., Staphylococcus sp. and Streptococcus sp. Learning Outcomes : 1.2(c) Describe the diversity of bacteria (based on cell shapes and Gram stain https://www.psoriasiseczema.com.au/psoriasis -relationship-viral-bacterial-fungal-infections/ http://qrbiology.weebly.com/cell-wall.html 25
(b) Gram Stain Learning Outcomes : 1.2(c) Describe the diversity of bacteria (based on cell shapes and Gram stain (ii) Gram-negative bacteria • More complex cell walls with thin peptidoglycan, with outer membrane that covers cell wall contains toxic lipopolysaccharides. • Stained pink, thin peptidoglycan cannot trap the crystal violet • e.g. Salmonella sp., Escherichia coli and Azotobacter sp. https://internal.lcc.edu/buildforward/catalog/ http://qrbiology.weebly.com/cell-wall.html 26
Gram-positive and Gram-negative bacteria Learning Outcomes : 1.2(c) Describe the diversity of bacteria (based on cell shapes and Gram stain 27
1.0 Biodiversity 1.1 Biodiversity and Classification 1.2 Domain Bacteria and Archaea 1.3 Diversity of Bacteria (Practical) 1.4 Domain Eukarya: Kingdom Protista 1.5 Domain Eukarya: Kingdom Fungi LECTURE 28
Learning outcomes : 1.4 Domain Eukarya: Kingdom Protista/Protoctista (a) State the unique characteristics of Protista. (b) State the classification of Protista based on unique feature: (i) Two major phyla of algae (photosynthetic pigment): ● Chlorophyta (Chlamydomonas sp.) ● Phaeophyta (Fucus sp.) (ii) Four major phyla of protozoa (locomotion): ● Euglenophyta (Euglena sp.) ● Rhizopoda (Amoeba sp.) ● Ciliophora (Paramecium sp.) ● Apicomplexa (Plasmodium sp.) 29
• Eukaryote • Diverse in cell organisation - most are unicellular, some are colonial unicellular & simple multicellular • Nutritional mode: autotrophic (e.g. algae), heterotrophic (e.g. most protozoa) or mixotrophic (e.g. Euglena sp.) • Mostly have one nucleus • Have membrane bounded organelles • Some reproduce asexually, others can also reproduce sexually • Need water-based environment UNIQUE CHARACTERISTICS - Protista Learning Outcomes : 1.4(a) State the unique characteristics of Protista https://biologyeducare.com/spirogyra/ http://biokabinet.weebly.com/pra382ivotinje.html http://www.microscopy-uk.org.uk/mag/indexmag.html?http://www.microscopyuk.org.uk/mag/wimsmall/sundr.html 30
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features. 31
● Phyla of ‘plant-like’ Protista that ○ carry out photosynthesis ○ have cell wall ● Photosynthetic pigments ○ chlorophyll a and b (Chlorophyta) ○ chlorophyll a, c, xanthophyll and other carotenoids (Phaeophyta) ● Carbohydrate storage: ○ starch (Chlorophyta) ○ laminarin and mannitol (Phaeophyta) ● Diversity in cell organisation – unicellular, simple multicellular e.g. filamentous, huge seaweeds ● Habitat: damp/wet environment - ocean, ponds, moist habitat with low light intensity CHARACTERISTICS OF ALGAE Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: LECTURE 1.4(b) State the classification of Protista based on the unique features. https://biology.stackexchange.com/questions/31777/howcan-green-algae-be-both-multicellular-and-unicellular https://www.britannica.com/science/Charophyceae https://geolearn.in/marine-ecosystems/ 32
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: LECTURE 1.4(b) State the classification of Protista based on the unique features. 33
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: Phylum Chlorophyta (green algae) e.g. Chlamydomonas sp. Found in variety of aquatic environments - mostly freshwater, salt water, damp soil. LECTURE Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features. https://mosys.univie.ac.at/research-andteaching/topics/clamydomonas-as-energy-resource/ https://inventioninovation.wordpress.com/2013/06/22/ chlamydomonas-with-labels/ 34
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: Phylum Phaeophyta (brown algae) e.g. Fucus sp. Almost exclusively marine. LECTURE Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features. https://www.alivingproof.com/products/bladderwrack-fucus http://premabotany.blogspot.com/2018/12/fucus.html 35
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: LECTURE 1.4(b) State the classification of Protista based on the unique features. 36
● In Latin, means “first/early/primitive animals” ● Unicellular protista ● Phyla of “animal-like” Protista ○ Mostly are holozoic that ingest food, have food vacuoles, except Euglena sp. that is mixotrophic - can be holozoic and autotrophic ○ Reproduce asexually by binary fission, but may reproduce sexually ● Diverse habitat - ocean, freshwater rivers and ponds, damp soils for free-living protozoa and in other organisms body for parasitic protozoa. ● Many species of protozoa are zooplanktons. PROTOZOA : UNIQUE CHARACTERISTICS Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: LECTURE 1.4(b) State the classification of Protista based on the unique features. 37
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PROTOZOA Phylum Euglenophyta, e.g. Euglena sp. Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: ● Have a flagellum on its anterior end ● Presence of chloroplast ● Absence of cell wall ● Mixotrophic LECTURE Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features. http://protist.i.hosei.ac.jp/pdb/images/Mastigophora/ Euglena/sp_4/sp_4.html https://rsscience.com/euglena/ 39
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: PROTOZOA Phylum Rhizopoda, e.g. Amoeba sp. ● Have pseudopodia (false feet) ● Holozoic ● Habitat: freshwater, ocean, living organism LECTURE Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features. 40
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: PROTOZOA Phylum Ciliophora, e.g. Paramecium sp. ● Have cilia for locomotion ● Habitat: fresh water & salt water ● Holozoic ● Have two nuclei ○ macronucleus ○ micronucleus LECTURE Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features. https://www.microscopemaster.com/paramecium.html https://www.britannica.com/science/Parameciumcaudatum 41
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: PROTOZOA: Phylum Apicomplexa, e.g. Plasmodium sp. LECTURE Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features. ● Have no locomotory extensions of the body (e.g. pseudopodia, flagella or cilia) ● Have an apical complex at their anterior end ● Mostly are parasitic https://www.inds.co.uk/product/plasmodiumfalciparum-blood-smear-with-more-gametocytes/ https://www.semanticscholar.org/paper/Plasmodium-sporozoitemolecular-cell-biology.-KappeBuscaglia/ca64c8f74fddec427667c60b2cae6f19f70a1d1a/figure/0 42
Learning Outcomes : 1.4(b) State the classification of Protista based on the unique features: 43
1.0 Biodiversity 1.1 Biodiversity and Classification 1.2 Domain Bacteria and Archaea 1.3 Diversity of Bacteria (practical) 1.4 Domain Eukarya: Kingdom Protista 1.5 Domain Eukarya: Kingdom Fungi 44
Learning outcomes : 1.5 Domain Eukarya: Kingdom Fungi (a) State the unique characteristics of Fungi (b) State the classification of Fungi phyla based on the spore-bearing structure : Zygomycota (Rhizopus sp.), Ascomycota (Penicillium sp.) Basidiomycota (Agaricus sp.) 45
Unique Characteristics 1. Multicellular eukaryotes 2. Body → mycelium (consisting of filamentous hyphae) 3. No chlorophyll 4. Have cell walls that contain chitin 5. Energy reserve : glycogen 6. Non motile 7. Heterotrophs that feed by absorption: i. Some are saprotrophic - Cells release digestive enzymes & then absorb the nutrient ii. Some are parasitic -Absorbs nutrients from living hosts Learning Outcomes : 1.5(a) State the unique characteristics of Fungi 46
iii. Several have mutualistic relationships - e.g. : fungi form an association with a green algae to form lichens – as aiding a plant in the uptake of mineral from the soil Learning Outcomes : 1.5(a) State the unique characteristics of Fungi lichens https://www.independenttree.com/is-lichen-on-trees-harmful/ 47 9. Reproduction : produce spores (asexually or sexually)
Vegetative Structure - Filamentous body plan - The filaments called hyphae - Hyphae : long, branched & threadlike, may absorb nutrients - form a mass called mycelium hyphae mycelium Learning Outcomes : 1.5(a) State the unique characteristics of Fungi 48
Learning Outcomes : 1.5(a) State the unique characteristics of Fungi • Types of hyphae : Coenocytic (non septate/aseptate): hyphae not divided into septums, multinucleated Septate : hyphae are divided into septa, individual cells containing one or more nucleus Pearson, 2018 49
Learning Outcomes : 1.5(a) State the unique characteristics of Fungi Specialized hyphae : HAUSTORIA -Haustoria : Nutrients absorbing hyphal tips that penetrate the tissues of host cells. -Present in mutualistic and parasitic fungi Function : extract nutrient from living plant 50