STUDENTS’ LEARNING OUTCOMES 

 After learning this chapter, the students will be able to:  

• Discuss the meaning of the words species and speciation. Describe the grouping of organisms into three domains: Archaea, Bacteria, and Eukarya. 
• Describe the classification of organisms in the Eukarya domain into the taxonomic system of kingdom, phylum, class, order, family, genus, and species. 
• Outline the characteristic traits of the kingdoms Monera, Protoctista, Fungi, Plantae, and Animalia. 
• Outline how viruses are classified. 
• Define the words ecosystem and niche. 
• Explain the different levels at which biodiversity can be measured. 
• Explain the value of random sampling in determining the biodiversity of an area. 
• Describe and use suitable methods to measure the distribution and abundance of organisms in an area. 

Biodiversity and classification are fundamental ideas in biology that provide insight into the vast array of life forms on Earth and their evolutionary relationships.  In this chapter, we will study the biodiversity, showing the variety of life at the genetic, species, and ecosystem levels.  We will also study the principles and methods of biological classification, which scientists use to organize and categorize organisms.  

 1.1- THREE-DOMAIN SYSTEM OF CLASSIFICATION 

1. Earlier Classification: Five-Kingdom System (Whittaker, 1969)                

Whittaker grouped all living organisms into five kingdoms:

• Monera – prokaryotes (bacteria)

• Protista

• Fungi

• Plantae

• Animalia

In this system:

• Prokaryotes = only the kingdom Monera

• Eukaryotes = the other four kingdoms

2. Woese’s Three-Domain System (1990)

Carl Woese discovered that the organisms previously lumped together as “prokaryotes” are actually two fundamentally different groups:

• Bacteria

• Archaea

Based on differences in ribosomal RNA, membrane composition, and other molecular features, Woese proposed three domains:

The Three Domains

1. Bacteria – true bacteria (prokaryotes)

2. Archaea – ancient prokaryotes with unique biochemistry

3. Eukarya – all eukaryotic organisms (protists, fungi, plants, animals)

3. Evolutionary Relationships

• Archaea and Bacteria both evolved from a common ancestor, but then split early in evolution.

• Archaea are more closely related to Eukaryotes (Eukarya) than they are to Bacteria.

• This means Eukarya evolved from within the Archaea lineage.

4. Phylogeny

• Phylogeny = the evolutionary history or relationships among organisms.

• A diagram showing these relationships is called a phylogenetic tree or evolutionary tree.

The evolutionary relationship among organisms is called  phylogeny. The diagram to show phylogeny, is called phylogenetic or evolutionary tree.

 

Domain Bacteria 

Introduction

In the five-kingdom system, the organisms now placed in Domain Bacteria were previously grouped under Kingdom Monera. They are known as the true bacteria and possess several characteristics that differentiate them from Archaea and Eukarya.

General Characteristics of Bacteria

1. Cell Structure

• Bacteria are prokaryotic, meaning they lack a true nucleus and membrane-bound organelles.

2. Cell Wall Composition

• Their cell walls contain peptidoglycan, a unique polymer that provides rigidity, shape, and protection.

3. Genetic Material

• Bacteria possess a single circular DNA chromosome located in the nucleoid region.

4. Plasmids

• Many bacteria contain plasmids—small circular DNA molecules that can move between bacteria, contributing to genetic diversity and antibiotic resistance.

5. Reproduction

• They reproduce asexually by binary fission, producing two identical daughter cells.

6. Nutritional Modes

• Autotrophs: make their own food (e.g., photosynthetic and chemosynthetic bacteria).

• Heterotrophs: obtain organic nutrients by feeding on other organisms or decaying matter.

7. Morphology (Shapes of Bacteria)

• Cocci – spherical

• Bacilli – rod-shaped

• Spirilla – spiral-shaped

• Vibrios – comma-shaped

8. Cell Arrangements

• Single cells

• Pairs (diplococci)

• Chains (streptococci)

• Clusters (staphylococci)

• Other arrangements depending on species

9. Flagella

• Many bacteria possess flagella, whip-like structures for movement.

10. Pili and Fimbriae

• Hair-like structures used for:

  • Surface attachment

  • Conjugation (transfer of genetic material)

11. Respiration Types

Bacteria can be:

• Obligate aerobes – need oxygen

• Obligate anaerobes – killed by oxygen

• Facultative anaerobes – grow with or without oxygen

• Microaerophiles – require low oxygen levels

• Aerotolerant anaerobes – don’t use oxygen but are not harmed by it

• Some perform fermentation when oxygen is absent

12. Extremophiles

Some bacteria live in extreme conditions:

• Thermophiles – high temperatures

• Halophiles – high salt concentrations

• Acidophiles – low pH

13. Pathogenicity

• Some bacteria cause diseases in humans, animals, and plants by producing toxins or other virulence factors.

14. Symbiosis

Many bacteria form beneficial or neutral relationships:

• Mutualism – both organisms benefit

• Commensalism – one benefits, the other is unharmed

  
  
  

Major Groups of Bacteria

Proteobacteria

Examples: Escherichia coli, Rhizobium, Helicobacter pylori

Firmicutes

Examples: Bacillus subtilis, Lactobacillus, Clostridium botulinum

Actinobacteria

Examples: Streptomyces, Mycobacterium tuberculosis

Cyanobacteria

Examples: Anabaena, Spirulina

Spirochaetes

Example: Treponema pallidum

Acidobacteria

Example: Acidobacterium

Aquificae

Example: Aquifex pyrophilus

Archaea were initially classified as a group of bacteria,  and were called archaebacteria.

 

Significance of Archaea

The archaeans that live in high acidity and alkalinity are a source of enzymes that can function under harsh conditions. For example, the enzymes of DNA replication have been extracted from such archaea.  These enzymes can work best at high temperatures and allow rapid cloning of  DNA  in the laboratory.  Similarly,  the methanogen archaeans are a vital part of sewage treatment.  They carry out anaerobic digestion and produce biogas. Acidophilic Archaea are used to extract metals such as gold, cobalt, and copper from ores in the mineral processing industry.

In humans, intestinal gas is largely the result of the metabolism of methanogens.

Domain Eukarya 

The domain Eukarya includes all organisms with eukaryotic cells, which differ fundamentally from prokaryotic cells found in Bacteria and Archaea.

General Characteristics of Domain Eukarya

1. Cell Structure

• Possess eukaryotic cells with a true nucleus enclosed by a nuclear membrane.

• Contain membrane-bound organelles, such as:

  • Mitochondria

  • Chloroplasts (in plants and algae)

  • Endoplasmic reticulum

  • Golgi apparatus

  • Lysosomes

  • Peroxisomes

• Have a cytoskeleton composed of microtubules, microfilaments, and intermediate filaments.

  • Provides structural support

  • Enables cell movement

  • Facilitates intracellular transport

2. Genetic Material

• DNA is arranged in multiple linear chromosomes housed inside the nucleus.

• Chromosomal DNA is associated with histone proteins, aiding in organization and gene regulation.

3. Reproduction

• Sexual reproduction is common, involving:

  • Meiosis, producing haploid gametes

  • Fertilization, restoring diploid state
    → results in genetic variation

• Asexual reproduction also occurs in many species through mitosis, producing genetically identical offspring.

4. Complex Cellular Organization

• Many eukaryotes are multicellular.

• Cells undergo differentiation, forming specialized:

  • Tissues

  • Organs

  • Organ systems

• Allows advanced physiological and structural complexity.

5. Evolutionary Relationships

• Eukaryotes are believed to have evolved through endosymbiosis:

  • Early eukaryotic ancestors engulfed certain prokaryotes (e.g., mitochondria, chloroplasts).

  • These cells became permanent, symbiotic organelles.

  • Evidence: own DNA, double membranes, bacterial-like ribosomes.

1.3 – Salient Features of Kingdoms of Domain Eukarya 

Domain Eukarya Overview

• Includes all eukaryotes with:

  • True nucleus

  • Membrane-bound organelles (mitochondria, ER, Golgi, etc.)

• Major kingdoms: Protista, Fungi, Plantae, Animalia

1. Kingdom Protista

General Features

• Eukaryotic organisms that may be:

  • Unicellular, colonial, filamentous, or simple multicellular

• Simple multicellular = no complex multicellular sex organs

• Highly diverse group

Major Groups

1. Protozoa (Animal-like protists)

• Unicellular, heterotrophic

• Examples: Amoeba, Paramecium, Plasmodium, Trypanosoma

2. Algae (Plant-like protists)

• Have cellulose cell walls

• Contain chlorophyll → autotrophic

• Examples: Euglena, diatoms

3. Fungi-like Protists

• Have hyphae-like structures

• Saprophytic

• Examples: slime molds (Myxomycota), water molds (Oomycota)

Disease-Causing Protists

• Plasmodium → malaria

• Entamoeba histolytica → amoebic dysentery

• Trypanosoma → sleeping sickness

2. Kingdom Fungi

General Features

• Eukaryotic, heterotrophic

• Unicellular or multicellular

• Cell wall made of chitin

• Obtain nutrition by absorption, not ingestion

• Examples: mushrooms, molds, rusts, smuts

Uses

• Food production: bread, cheese, beer

• Medicine: Penicillin from Penicillium

• Symbiotic associations:

  • Lichens

  • Mycorrhizae

Major Groups

1. Zygomycota

• Hyphae without septa

• Example: Rhizopus (bread mold)

2. Ascomycota

• Largest group; septate hyphae

• Examples: morels, truffles, yeasts, Neurospora, cup fungi

3. Basidiomycota

• Septate hyphae

• Examples: mushrooms, toadstools, puffballs, jelly fungi, bracket fungi, rusts, smuts

3. Kingdom Plantae

General Features

• Eukaryotic, multicellular

• Cell wall made of cellulose

• Autotrophic (photosynthesis)

• Develop from embryos

• Examples: mosses, ferns, conifers, flowering plants

Major Groups

1. Non-vascular Plants (Bryophytes)

• No xylem or phloem

• Examples: mosses, liverworts, hornworts

2. Vascular Plants

• Have conducting tissues → xylem & phloem

• Two types:

  • Seedless vascular plants → e.g., ferns

  • Seed plants → e.g., conifers, flowering plants

1.4 – Classification of Kingdom Animalia

Phylum 1: Porifera (Sponges)

General Features

• Commonly called sponges.

• Mostly marine; few freshwater species.

  • Examples:

    • Marine: Leucosolenia, Euplectella (Venus’ flower basket)

    • Freshwater: Spongilla

• No true tissues → cellular level of organization.

• Asymmetrical or radially symmetrical.

• No nervous system.

Body Structure

• Body contains numerous pores called ostia (water enters).

• Water exits through a large opening called osculum.

• Three main layers:

  • Pinacocytes → thin, flat outer cells.

  • Mesohyle → jelly-like middle layer containing amoeboid cells.

  • Choanocytes (collar cells) → inner layer lining spongocoel; help in feeding and water circulation.

• Skeleton made of:

  • Calcium carbonate or

  • Silica spicules (minute needle-like structures).

Reproduction

• Mostly asexual:

  • Budding

  • Regeneration

• Formation of gemmules (resistant capsules):

  • Released when parent sponge dies.

  • In favorable conditions, amoeboid cells emerge to develop into a new sponge.

Human Use

• Commercial sponges prepared by cleaning, drying, and removing all cells from natural sponges.

Phylum Cnidaria

General Features

• Mostly marine; few freshwater species (e.g., Hydra, some jellyfish).

• Many are colonial (e.g., Obelia, corals, sea fans).

• Mostly sessile (attached), but some are motile (e.g., jellyfish).

• Corals:

  • Colonial cnidarians.

  • Produce calcium carbonate exoskeleton → form coral islands and coral reefs.

Body Structure

• Radial symmetry.

• Diploblastic:

  • Epidermis (from ectoderm)

  • Gastrodermis (from endoderm)

  • Mesoglea: jelly-like layer between the two.

• Have cnidocytes → stinging cells.

  • Contain nematocysts, used for defense and capturing prey.

• Body cavity: Gastrovascular cavity (enteron).

  • Single opening → mouth (also functions as anus).

  • Surrounding tentacles aid in capturing food.

• Sac-like digestive system (one opening only).

Nervous & Other Systems

• Nervous system is a nerve net → no brain or spinal cord.

• No specialized respiratory, excretory, or transport systems.

Body Forms

1. Polyp

   • Cylindrical, sessile.

   • Attached at the aboral end.

   • Reproduce asexually.

2. Medusa

   • Umbrella-shaped, free-swimming.

   • Reproduce sexually.

Examples

• Hydra, Obelia, Jellyfish, Sea anemones, Corals, Sea fans

Corals are colonial cnidarians. They produce a hard exoskeleton

of  Calcium carbonate.  The skeleton makes coral islands and coral reefs.

• 

Phylum Platyhelminthes

General Features

• Commonly called flatworms.

• Unsegmented, soft-bodied, and dorsoventrally flattened.

• Mostly free-living (e.g., Planaria).

• Some are endoparasites of humans and animals:

  • Liver fluke, tapeworm, blood fluke.

Body Organization

• Triploblastic:

  • Derived from 3 layers → ectoderm, mesoderm, endoderm.

• Acoelomate:

  • No body cavity; space filled with parenchyma (loose connective tissue).

• Bilateral symmetry with distinct:

  • Left/right sides

  • Dorsal/ventral sides

Organ Systems

Digestive, Respiratory, and Circulatory

• No respiratory system → gas exchange through body surface.

• No circulatory (transport) system.

• Digestive system varies:

  • Some have a simple gastrovascular cavity.

  • Tapeworms have no digestive system (absorb nutrients).

Excretory System

• Network of protonephridia (tubular system).

• Tubules end in flame cells:

  • Cilia beat to draw fluid in.

  • Waste exits through nephridiopores.

Nervous System

• Cerebral ganglia at anterior end (simple brain).

• Longitudinal nerve cords connected by transverse branches (ladder-like system).

• Many free-living forms have eyespots for light detection.

Reproduction

• Asexual reproduction:

  • By fission → body constricts and divides; each part regenerates missing structures.

• Sexual reproduction:

  • Most are hermaphrodites (bisexual).

Examples

• Planaria, Liver fluke (Fasciola),

• Tapeworm (Taenia), Blood fluke (Schistosoma)

Phylum Nematoda

General Characteristics

• Commonly called roundworms.

• Body elongated, cylindrical, unsegmented, with tapered ends.

• Found free-living (water, soil) e.g., Caenorhabditis elegans.

• Many are parasitic: Ascaris, hookworm, pinworm, whipworm.

• Part of Aschelminths group; Nematoda is the representative phylum.

Body Organization

• Triploblastic (three germ layers).

• Bilateral symmetry.

• Pseudocoelomate — fluid-filled pseudocoelom, not a true coelom.

• Tough cuticle present; molts periodically.

Digestive System

• Complete digestive tract (tube-within-a-tube).

• Has two openings:

  • Mouth (anterior)

  • Anus (posterior)

• Parasitic species often have simplified digestive systems.

Excretory System

• Excretory system includes:

  • Protonephridia

  • Two longitudinal excretory canals (join anteriorly → single canal)

  • Single canal opens via nephridiopore on ventral side.

Nervous System

• Nerve ring around pharynx.

• Four longitudinal nerve cords.

• Sensory papillae (hair-like sensory organs) on the lips.

Other Systems

• No respiratory system (gas exchange through body surface).

• No circulatory system (nutrients transported via pseudocoelomic fluid).

Reproduction

• Dioecious (unisexual) — separate male and female individuals.

  • Males: testes

  • Females: ovaries

• Sexual reproduction; internal fertilization.

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