outline the characteristic features of the kingdoms Protoctista, Fungi, Plantae and Animalia

18 Classification, Biodiversity and Conservation

Learning outcomes (LOs)

• LO1 – Explain the three‑domain system and the five‑kingdom classification and describe the hierarchical taxonomic ranks. (AO1)
• LO2 – Identify and compare the characteristic features of the kingdoms Monera, Protoctista, Fungi, Plantae and Animalia, linking these features to cell structure, metabolism and life‑cycle concepts studied elsewhere in the syllabus. (AO1, AO2)
• LO3 – Interpret molecular‑based phylogenetic trees and evaluate how DNA/RNA data are used in modern systematics. (AO2, AO3)
• LO4 – Analyse biodiversity indicators for each kingdom and discuss the implications for conservation and sustainable use. (AO2, AO3)
• LO5 – Design and evaluate a simple experimental investigation that demonstrates a taxonomic or ecological principle related to the five kingdoms. (AO3)

18.1 The three‑domain system

• Archaea – Membrane lipids are ether‑linked; rRNA sequences distinct from Bacteria; extremophilic metabolism.
• Bacteria (Monera) – Ester‑linked lipids, peptidoglycan cell wall; diverse metabolisms (photo‑, chemo‑, litho‑autotrophy and heterotrophy).
• Eukarya – Membrane‑bound organelles, linear chromosomes, introns; includes the five kingdoms used in the Cambridge syllabus.

18.2 Five‑kingdom classification (within Eukarya)

1. Protoctista (Protista)
2. Fungi
3. Plantae
4. Animalia
5. Monera (Bacteria) – covered in Topic 2 but retained here for completeness.

Taxonomic hierarchy (broad → specific)

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

Each successive rank reflects increasing similarity in morphology, physiology and, increasingly, DNA sequence data.

18.3 Characteristic features of the five kingdoms

18.3.1 Monera (Bacteria)

• Cell type: Prokaryotic – no nucleus or membrane‑bound organelles.
• Cell wall: Peptidoglycan (Gram‑positive) or thin peptidoglycan with outer membrane (Gram‑negative).
• Nutrition: Extremely diverse – photo‑autotrophic (cyanobacteria), chemo‑autotrophic (nitrifying bacteria), chemo‑heterotrophic (most pathogens), and mixotrophic species.
• Reproduction: Asexual binary fission; some undergo specialised processes such as budding, spore formation or conjugation (horizontal gene transfer).
• Habitat: Ubiquitous – soil, water, extreme environments (hot springs, deep‑sea vents), symbiotic (gut flora, nitrogen‑fixing nodules).
• Examples: Escherichia coli (intestinal bacterium), Streptomyces coelicolor (soil antibiotic producer), Synechocystis (cyanobacterium).

18.3.2 Protoctista (Protista)

• Cell type: Mostly unicellular; some simple multicellular forms (filamentous algae, slime moulds).
• Cell wall: Variable – absent, silica‑based (diatoms), cellulose (green algae) or cellulose‑like (some slime moulds).
• Nutrition: Autotrophic (photosynthetic algae), heterotrophic (amoebae, ciliates) or mixotrophic (e.g., Euglena).
• Reproduction: Asexual (binary fission, budding, fragmentation) and sexual (gamete formation, conjugation, syngamy).
• Habitat: Aquatic (freshwater & marine) and moist terrestrial environments; many are planktonic.
• Examples: Paramecium caudatum, Euglena gracilis, brown alga Fucus vesiculosus.

18.3.3 Fungi

• Cell type: Predominantly multicellular hyphae forming a mycelium; unicellular yeasts also common.
• Cell wall: Chitin (β‑(1→4)‑linked N‑acetylglucosamine polymer).
• Nutrition: Heterotrophic – external digestion of organic matter followed by absorption (saprotrophic, parasitic, mutualistic).
• Reproduction: Asexual – spores (conidia, sporangiospores) or budding; Sexual – specialised spores after meiosis (basidiospores, ascospores).
• Habitat: Soil, decaying organic matter, symbiotic associations (mycorrhizae with plants, lichens with algae).
• Examples: Bread mould Rhizopus stolonifer, baker’s yeast Saccharomyces cerevisiae, mushroom Agaricus bisporus.

18.3.4 Plantae

• Cell type: Multicellular eukaryotes with specialised tissues (dermal, vascular, ground).
• Cell wall: Cellulose fibres embedded in a matrix of hemicellulose and pectin.
• Chloroplasts: Contain chlorophyll a + b and carotenoids; origin by primary endosymbiosis.
• Nutrition: Autotrophic – photosynthetic conversion of CO₂ and H₂O into carbohydrates; some non‑vascular plants also absorb dissolved organic matter.
• Reproduction: Alternation of generations (haploid gametophyte ↔ diploid sporophyte); sexual (flowers, cones) and asexual (runners, tubers, apomixis).
• Habitat: Predominantly terrestrial; also aquatic (seagrasses, water lilies).
• Examples: Model angiosperm Arabidopsis thaliana, conifer Pinus sylvestris, green alga Chlamydomonas reinhardtii (basal plant analogue).

18.3.5 Animalia

• Cell type: Multicellular eukaryotes with true tissues, organs and organ systems.
• Cell wall: Absent – cells surrounded only by a flexible plasma membrane.
• Nutrition: Heterotrophic – ingestion of solid or liquid food followed by internal digestion (extracellular enzymes).
• Motility: Most are motile at some life stage (ciliary larvae, muscular movement).
• Reproduction: Predominantly sexual (gametes, fertilisation) with diverse developmental patterns (cleavage, gastrulation, metamorphosis); some asexual modes (budding, fragmentation, parthenogenesis).
• Habitat: Virtually all environments – terrestrial, freshwater, marine, parasitic niches.
• Examples: Human Homo sapiens, fruit fly Drosophila melanogaster, freshwater sponge Spongilla.

18.4 Comparative summary of the five kingdoms

18.5 Molecular systematics and phylogenetic trees

• Common DNA/RNA markers: 18S rRNA, 28S rRNA, mitochondrial COI, chloroplast rbcL, ITS regions.
• Workflow:
  1. Extract DNA → PCR amplify marker → sequence.
  2. Align sequences → calculate genetic distances.
  3. Construct tree using neighbour‑joining, maximum‑parsimony or Bayesian inference.
• Tree interpretation:
  • Branch length ≈ amount of molecular change (molecular‑clock hypothesis).
  • Node = most recent common ancestor; monophyletic groups share a single ancestor.
  • Paraphyletic / polyphyletic groups indicate that traditional classifications need revision.
• Case study (AO3): rbcL and 18S rRNA sequences show that brown algae (Phaeophyceae) and diatoms belong to the same SAR super‑group, prompting a re‑organisation of the Protista kingdom.

18.6 Biodiversity indicators and conservation relevance

18.7 Practical / data‑analysis activity (AO3)

Title: “Evaluating a universal 18S rRNA primer set across the five kingdoms”.

1. Collect small tissue samples of: Euglena (Protoctista), baker’s yeast (Saccharomyces cerevisiae, Fungi), spinach leaf (Spinacia oleracea, Plantae), earthworm tissue (Lumbricus terrestris, Animalia) and a bacterial culture (E. coli, Monera).
2. Extract genomic DNA using a commercial kit; include a negative control.
3. Set up PCR with a conserved 18S rRNA primer pair (for eukaryotes) and a 16S rRNA primer pair (for bacteria). Run products on a 1.5 % agarose gel.
4. Record band intensity (qualitative) and, where facilities allow, purify and sequence the amplicons.
5. Interpretation:
   • Successful amplification in all eukaryotic samples demonstrates the utility of 18S rRNA for broad‑scale phylogenetics.
   • Weak or absent bands may result from secondary metabolites (e.g., polyphenols in plants) inhibiting PCR; discuss troubleshooting (e.g., additional purification, BSA addition).
   • Compare the bacterial 16S result with the eukaryotic 18S to highlight the need for domain‑specific markers.
6. Link to LO3 (interpretation of molecular data) and LO5 (design & evaluation of an experiment). (AO3)

18.8 Suggested diagram