Biological Classification

Biological Classification

In this chapter, we will explore the diversity of life through biological classification, from early attempts to the modern five kingdom system, covering Monera, Protista, Fungi, Plantae, Animalia, and unique entities like viruses, viroids, prions, and lichens. So let’s get started.

Early Classification Attempts

• Aristotle: Used simple features like trees, shrubs, herbs for classifying plants; and red blood vs no red blood as a criteria for animals.
• Linnaeus: Introduced the Two Kingdom system (Plantae and Animalia).

Limitations of the Two Kingdom System

• Didn’t distinguish between:
  • Eukaryotes and prokaryotes.
  • Unicellular and multicellular organisms.
  • Photosynthetic and non-photosynthetic organisms.
• Many organisms didn’t fit well into Plantae or Animalia.

Example of Classification Changes from old system vs. new

• Old System: included Algae, fungi, bacteria, etc., all grouped under plants due to the presence of cell walls.
• New System: Recognizes differences like prokaryotic vs. eukaryotic, unicellular vs. multicellular, and autotrophic vs. heterotrophic.

Need for Better Classification

• Consideration of more characteristics like cell structure, mode of nutrition, habitat, reproduction, and evolutionary relationships was required.
• Modern classification systems have evolved to reflect these complexities.

Five Kingdom Classification by R.H. Whittaker (1969)

1. Monera: Prokaryotic organisms (bacteria and cyanobacteria).
2. Protista: Unicellular eukaryotes (e.g., Chlamydomonas, Amoeba).
3. Fungi: Heterotrophic organisms with chitin in cell walls.
4. Plantae: Multicellular, autotrophic green plants with cellulose cell walls.
5. Animalia: Multicellular, heterotrophic organisms without cell walls.

Characters	Monera	Protista	Fungi	Plantae	Animalia
Cell type	Prokaryotic	Eukaryotic	Eukaryotic	Eukaryotic	Eukaryotic
Cell wall	Noncellulosic (Polysaccharide + amino acid)	Present in some	Present with chitin	Present (cellulose)	Absent
Nuclear membrane	Absent	Present	Present	Present	Present
Body organization	Cellular	Cellular	Multicellular/ loose tissue	Tissue/organ	Tissue/organ/ organ system
Mode of nutrition	Autotrophic (chemosynthetic and photosynthetic) and Heterotrophic (saprophytic/ parasitic)	Autotrophic (photosynthetic) and Heterotrophic	Heterotrophic (saprophytic/ parasitic)	Autotrophic (photosynthetic)	Heterotrophic (holozoic/ saprophytic, etc.)

Characteristics Considered under 5 Kingdom Classification

• Cell structure
• Body organization
• Mode of nutrition
• Reproduction
• Phylogenetic relationships (evolutionary history)

Further Advances in Classification

• Three-Domain System: Divides Kingdom Monera into two domains and overall includes six kingdoms (but still 5 kingdom classification is most popular).

Future of Classification

• Will continue to evolve with better understanding of characteristics and evolutionary relationships.

Kingdom Monera

Bacteria: The Basics

• Abundance: Most common microorganisms, found everywhere.
• Habitat: Soil, extreme environments (hot springs, deserts, snow, deep oceans), on or in organisms as parasites.

Shapes of Bacteria

• Coccus: Spherical.
• Bacillus: Rod-shaped.
• Vibrium: Comma-shaped.
• Spirillum: Spiral.

Metabolic Diversity

• Autotrophic Bacteria: Make their own food.
  • Photosynthetic Autotrophs: Use sunlight for making food.
  • Chemosynthetic Autotrophs: Use chemicals energy for making food.
• Heterotrophic Bacteria: Depend on others for food, including dead organic matter.

Types of Bacteria

1. Archaebacteria (Primitive Bacteria)

• Habitats: Extreme environments (salty areas, hot springs, marshes).
• Cell Wall: Unique structure enabling survival in harsh conditions.
• Examples:
  • Halophiles: Salt-loving or living in extreme salty areas.
  • Thermoacidophiles: Heat and acid-loving.
  • Methanogens: Produce methane in animal guts (e.g., cows).

2. Eubacteria (True Bacteria)

• Characteristics: Rigid cell wall, some are motile due to flagella.
• Cyanobacteria (Blue-Green Algae):
  • Have ‘chlorophyll a’ similar to green plants. 💪
  • Photosynthetic autotrophs.
  • Form blooms in polluted waters.😢
  • Some (e.g., Nostoc, Anabaena) can fix atmospheric nitrogen in specialized cells (heterocysts). 👍
• Chemosynthetic Autotrophs:
  • Use inorganic substances for energy by their oxidation.
  • Their reactions (role) Important for nutrient recycling (nitrogen, phosphorus, iron, sulfur).

Heterotrophic Bacteria

• Decomposers: Most are Decomposers and break down dead matter.
• Uses: Curd making, antibiotic production, nitrogen fixation in legume roots.
• Pathogens: Some are Pathogens, cause diseases like cholera, typhoid, tetanus, citrus canker.

Reproduction in Bacteria

• Fission: Main method (splitting into two).
• Spores: Formed under unfavorable conditions.
• DNA Transfer: Primitive sexual reproduction in bacteria (bacterial conjugation).

Mycoplasma

• Characteristics: No cell wall, smallest living cells.
• Survival: Can live without oxygen i.e. Anaerobic.
• Pathogenic: Cause diseases in animals and plants.

Kingdom Protista

Overview

• Definition: All single-celled eukaryotes.
• Habitat: Primarily aquatic.
• Features: Well-defined nucleus, membrane-bound organelles, some have flagella or cilia.
• Reproduction: Asexual and sexual (cell fusion and zygote formation).
• Protists are diverse eukaryotic microorganisms that share traits with plants, animals, and fungi, serving as an evolutionary link among these kingdoms.

Groups in Protista

1. Chrysophytes

• Includes: Diatoms and golden algae (desmids).
• Habitat: Freshwater and marine environments.
• Characteristics: Microscopic, float in water (plankton), photosynthetic thus chief producers of ocean.
• Cell Wall: Diatoms have two thin overlapping (fitting like a soap box) silica shells (indestructible).
• Importance: Main producers in oceans; diatomaceous earth (Diatoms’ cell wall deposition over time) used for polishing, filtration of oils and syrups.

2. Dinoflagellates

• Habitat: Mostly marine, photosynthetic.
• Colors: Yellow, green, brown, blue, or red (due to different pigments).
• Cell Wall: Stiff cellulose plates.
• Movement: Two flagella (one longitudinal, one transverse).
• Example: Gonyaulax (causes red appearance tides, can release toxins harmful to marine life).

3. Euglenoids

• Habitat: Freshwater, stagnant water.
• Cell Wall: None; instead, a flexible protein-rich layer called pellicle (provides flexibility).
• Movement: Two flagella (one short, one long).
• Nutrition: Photosynthetic in sunlight; heterotrophic without sunlight.
• Example: Euglena.
• The Photosynthesis pigments are exactly same as in higher plants.

4. Slime Moulds

• Nutrition: Saprophytic (feeds on decaying organic matter).
• Movement: Creeps along decaying material.
• Aggregation: Forms plasmodium (a large, single-celled, multinucleate mass) under suitable conditions.
• Reproduction: Forms spores during unfavorable conditions; spores are resistant and dispersed by air.

5. Protozoans

• Nutrition: Heterotrophic (predators or parasites).
• Primitive Relatives: of Animals i.e. Protozoans are considered the earliest ancestors of animals.
• Groups:
  • Amoeboid Protozoans: Move using pseudopodia (e.g., Amoeba). Some have silica shells. Example: Entamoeba (parasite).
  • Flagellated Protozoans: Have flagella, free-living or parasitic. Example: Trypanosoma (causes sleeping sickness).
  • Ciliated Protozoans: Move using cilia, aquatic, have a gullet (cavity) for feeding. Example: Paramoecium.
  • Sporozoans: Infectious spore-like stage in life cycle. Example: Plasmodium (causes malaria)

Kingdom Fungi

Overview

• Nature: Unique kingdom of heterotrophic organisms.
• Diversity: Varied in shape and habitat.
• Examples:
  • Common mushrooms and toadstools
  • Fungi on moist bread and rotten fruits
  • Yeast (unicellular, used in bread and beer making)
  • Penicillium (source of antibiotics)
  • Puccinia (causes wheat rust)

Habitat

• Occurrence: Found in air, water, soil, on animals, and plants.
• Preference: Warm and humid places.

Nutrition

• Saprophytes: Absorb nutrients from dead organic matter.
• Parasites: Depend on living hosts.
• Symbionts: Live in association with other organisms (e.g., lichens with algae, mycorrhiza with plant roots).
• Reserved food is glycogen.

Structure

• Body: Filamentous, made up of long threads called hyphae.
• Network: Hyphae form a network called mycelium.
• Types of Hyphae:
  • Coenocytic: Continuous tubes with many nuclei without cross walls..
  • Septate: Hyphae divided by cross walls, creating distinct, individual cells.
• Cell Wall: Made of chitin and polysaccharides.

Reproduction

• Vegetative: Fragmentation, fission, budding.
• Asexual: Spores like conidia, sporangiospores, zoospores.
• Sexual: Spores like oospores, ascospores, basidiospores.
• Sexual Cycle:
  • Plasmogamy: Fusion of cell (gamete) contents.
  • Karyogamy: Fusion of two nuclei.
  • Meiosis: Formation of haploid spores from Zygote.

Major Classes of Fungi

1. Phycomycetes

• Habitat: Aquatic, moist places, parasites on plants.
• Mycelium: Aseptate, coenocytic.
• Reproduction:
  • Asexual: Zoospores (motile), aplanospores (non-motile).
  • Sexual: Zygospore (formed by fusion of gametes).
• Examples: Mucor, Rhizopus (bread mould), Albugo.

2. Ascomycetes (Sac-fungi)

• Forms: Mostly multicellular (e.g., Penicillium), some unicellular (e.g., yeast).
• Nature: Saprophytic, decomposers, parasitic, coprophilous (growing on dung).
• Mycelium: Branched, septate.
• Reproduction:
  • Asexual: Conidia (produced on conidiophores – A specialized fungal structure).
  • Sexual: Ascospores (produced in asci/ascus – A sac-like structure, within ascocarps).
• Examples: Aspergillus, Claviceps, Neurospora.
• Neurospora is utilized in biochemical and genetic research.
• Morels and truffles are edible.

3. Basidiomycetes

• Forms: Mushrooms, bracket fungi, puffballs.
• Habitat: Soil, logs, tree stumps, living plants (as parasites).
• Mycelium: Branched, septate.
• Reproduction:
  • Asexual: Asexual spores are rare; instead, vegetative reproduction through fragmentation is common.
  • Sexual: Basidiospores (produced on basidia within basidiocarps).
• Examples: Agaricus (mushroom), Ustilago (smut), Puccinia (rust fungus).

4. Deuteromycetes (Imperfect fungi)

• Nature: Only asexual or vegetative phases known thus called imperfect. Once their perfect sexual stages are identified, they are often categorized as ascomycetes or basidiomycetes.
• It is also possible that Asexual and vegetative stages may be named under deuteromycetes and the sexual stage under another class. Once linkages are established, the fungi are correctly identified and reclassified out of deuteromycetes.
• Reproduction: Conidia (asexual spores).
• Mycelium: Septate, branched.
• Role: Saprophytes, parasites, decomposers (mineral cycling).
• Examples: Alternaria, Colletotrichum, Trichoderma.

Class	Habitat / Nature	Mycelium	Asexual Reproduction	Sexual Reproduction	Examples
Phycomycetes	Aquatic, moist places, plant parasites	Aseptate, coenocytic	Zoospores (motile), aplanospores (non-motile)	Zygospore (fusion of gametes)	Mucor, Rhizopus (bread mould), Albugo
Ascomycetes	Mostly saprophytic, decomposers, parasitic, coprophilous	Branched, septate	Conidia (on conidiophores)	Ascospores (in asci within ascocarps)	Penicillium, Aspergillus, Claviceps, Neurospora, Morels, Truffles
Basidiomycetes	Soil, logs, tree stumps, living plants (parasites)	Branched, septate	Rare; vegetative reproduction by fragmentation	Basidiospores (on basidia within basidiocarps)	Agaricus (mushroom), Ustilago (smut), Puccinia (rust fungus)
Deuteromycetes	Saprophytes, parasites, decomposers	Septate, branched	Conidia	None known; reclassified when sexual stage identified	Alternaria, Colletotrichum, Trichoderma

Kingdom Plantae

Overview

• Nature: Eukaryotic, chlorophyll-containing Photosynthetic organisms (plants).
• Types:
  • Insectivorous plants: Bladderwort, Venus flytrap.
  • Parasites: Cuscuta.
• Cell Structure: Eukaryotic cells with chloroplasts and cellulose cell walls.

Groups of Plants

• Algae: Simple, usually aquatic plants.
• Bryophytes: Mosses and liverworts.
• Pteridophytes: Ferns and their relatives.
• Gymnosperms: Conifers and cycads.
• Angiosperms: Flowering plants.

Life Cycle

• Phases:
  • Diploid sporophytic phase.
  • Haploid gametophytic phase.
• Alternation of Generations: These phases alternate, varying in length and dependency among different plant groups.

Kingdom Animalia

Overview

• Nature: Multicellular, heterotrophic eukaryotic organisms, no cell wall.
• Dependence: Directly or indirectly depend on plants for food.
• Cell Structure: No cell walls, cells store food as glycogen or fat.

Characteristics

• Nutrition: Holozoic (ingestion of food).
• Growth: Definite growth pattern into adults with a specific shape and size.
• Mechanisms: Advanced sensory and neuromotor mechanisms in higher forms.
• Locomotion: Most animals can move.

Reproduction

• Sexual: Copulation (mating) of male and female, followed by embryological development.

Viruses, Viroids, Prions, and Lichens

Viruses

• Nature: Non-cellular (acellular) organisms, inert outside a living cell ,only active metabolically when inside host body.
• Living or Non-living?: Debatable, as they lack a cell structure.
• Discovery:
  • Dmitri Ivanowsky (1892): Found viruses causing mosaic disease in tobacco.
  • M.W. Beijerinek (1898): Called infectious plant fluid “Contagium vivum fluidum.”
  • W.M. Stanley (1935): Crystallized viruses, showing they are mainly protein.
• Structure:
  • Genetic material (RNA or DNA, never both) inside a protein coat called a capsid thus called nucleoprotein.
  • Capsid made of subunits called capsomeres.
• Types:
  • Plant viruses: Usually single-stranded RNA.
  • Animal viruses: Single or double-stranded RNA or double-stranded DNA.
  • Bacteriophages: Double-stranded DNA.
• Diseases: Cause mumps, smallpox, herpes, influenza, AIDS in humans, and various plant diseases thus making them obligate (compulsorily) parasites.

Viroids

• Discovery: T.O. Diener (1971).
• Nature: Smaller than viruses, consist of free RNA without a protein coat.
• Disease: Causes potato spindle tuber disease.

Prions

• Nature: Infectious agents made of abnormally folded proteins.
• Diseases:
  • Bovine Spongiform Encephalopathy (BSE): Mad cow disease in cattle.
  • Creutzfeldt-Jakob Disease (CJD): Human variant.

Lichens

• Nature: Symbiotic association between algae (phycobiont) and fungi (mycobiont).
• Function:
  • Algae provide food via photosynthesis.
  • Fungi provide shelter and absorb nutrients and water.
• Pollution Indicator: Do not grow in polluted areas.

Chapter Summary:

• Aristotle first proposed biological classification of plants and animals based on simple morphological characters.
• Linnaeus classified all living organisms into two kingdoms: Plantae and Animalia.
• Whittaker proposed a five-kingdom classification: Monera, Protista, Fungi, Plantae, and Animalia.
• The five-kingdom classification criteria include cell structure, body organization, mode of nutrition, reproduction, and phylogenetic relationships.
• In the five-kingdom classification:
  • Bacteria are in Kingdom Monera.
  • Bacteria are found everywhere and have extensive metabolic diversity.
  • Bacteria can be autotrophic or heterotrophic.
• Kingdom Protista includes single-celled eukaryotes like Chrysophytes, Dinoflagellates, Euglenoids, Slime-moulds, and Protozoans.
  • Protists have a defined nucleus and membrane-bound organelles.
  • Protists reproduce both asexually and sexually.
• Kingdom Fungi members show great diversity in structure and habitat.
  • Most fungi are saprophytic.
  • Fungi reproduce asexually and sexually.
  • Four classes of fungi: Phycomycetes, Ascomycetes, Basidiomycetes, and Deuteromycetes.
• Kingdom Plantae includes all eukaryotic, chlorophyll-containing organisms like algae, bryophytes, pteridophytes, gymnosperms, and angiosperms.
  • Plants have a life cycle with alternation of generations (gametophytic and sporophytic).
• Kingdom Animalia includes heterotrophic, eukaryotic, multicellular organisms without a cell wall.
  • Animals have holozoic nutrition.
  • Animals reproduce mostly by sexual means.
• Viruses, viroids, and lichens are not included in the five-kingdom classification system.