Biological Classification

Relationships in the historical five-kingdom model

Historical five-kingdom system
- Monera
  Historical diagram: first cells → Monera → eukaryotic branch.
- Eukaryotic branch
  - Protista
  - Fungi
  - Animalia
  - Plantae

Viruses are acellular and are not assigned to one of the five cellular kingdoms.

Historical five-kingdom system

Viruses are acellular and are not assigned to one of the five cellular kingdoms.

Monera
Historical diagram: first cells → Monera → eukaryotic branch.
Eukaryotic branch
- Protista
- Fungi
- Animalia
- Plantae

Kingdom	Organisation	Nutrition and reserves	Distinguishing features
Monera	Prokaryotic; bacteria are its sole members.	Photosynthetic autotrophs, chemosynthetic autotrophs or heterotrophs.	Bacteria occur almost everywhere.
Protista	Primarily unicellular eukaryotes.	Variable nutrition.	Forms a link between plants, animals and fungi.
Fungi	Eukaryotic; mostly multicellular.	Heterotrophic by absorption; saprophytic, parasitic or symbiotic. Reserve food: glycogen.	Achlorophyllous, spore-forming and non-vascular. True fungal walls contain chitin and glucans; some cellulose-walled organisms were included with fungi in older classifications.
Animalia	Multicellular and eukaryotic; cell walls are absent.	Non-green heterotrophs; holozoic nutrition by ingestion. Reserve food: glycogen or fats.	Sexual reproduction involves gamete fusion followed by embryological development; copulation occurs in some groups.
Plantae	Eukaryotic and mostly multicellular; most plants bear chlorophyll.	Most plants are green and photosynthetic; nonphotosynthetic exceptions occur.	Includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms.

In land plants, the life cycle alternates between a diploid sporophytic phase and a haploid gametophytic phase. Algal life cycles vary.

Kingdom Monera

Bacteria
- Archaebacteria
  - Halophiles
  - Thermoacidophiles
  - Methanogens
- Eubacteria

Bacteria

Archaebacteria
- Halophiles
- Thermoacidophiles
- Methanogens
Eubacteria

Halophiles

Salt-loving organisms.

Thermoacidophiles

Found in hot springs.

Methanogens

Found in marshes and in the gut of ruminant animals; they produce methane gas.

Nutrition and roles of bacteria

Nutritional group	Features and examples
Photosynthetic autotrophs	Cyanobacteria, also called blue-green algae (BGA). Some, such as Anabaena and Nostoc, have specialised cells called heterocysts for nitrogen fixation.
Chemosynthetic autotrophs	Oxidise inorganic substrates such as nitrite and ammonia, using the released energy for ATP production. They help recycle N, P, Fe and S.
Heterotrophic bacteria	Include decomposers and bacteria involved in curd-making, antibiotic production and N₂ fixation. Other heterotrophic bacteria cause diseases such as typhoid, tetanus and citrus canker.

An algal bloom is a rapid increase in the abundance of algae or cyanobacteria in a water body.

Cyanobacterial blooms can appear as abundant blue-green growth over the surface of polluted water bodies.

Some cyanobacterial blooms produce neurotoxins; dense blooms can deplete dissolved oxygen and make water unfit for use.

Mycoplasmas completely lack a cell wall and are among the smallest self-replicating cells.

Some mycoplasmas can survive without oxygen, while others are obligately aerobic.

Some mycoplasmas cause disease in animals; related phytoplasmas cause disease in plants.

Kingdom Protista

The diagrams compare a diatom shell, a flagellated Euglena, a plasmodial slime mould and a ciliated Paramecium. — Protist examples

Group	Habitat and nutrition	Structure and behaviour	Examples and significance
Chrysophytes	Freshwater or marine; photosynthetic microscopic plankton.	In diatoms, silica-rich cell walls resist decay; their two overlapping halves fit together like a soap box.	In this historical grouping, chrysophytes include diatoms, golden algae and desmids; desmids are green algae, distinct from golden algae. Accumulated diatom walls form diatomaceous material used for polishing and filtration of oils and syrups.
Dinoflagellates	Most are marine; freshwater forms also occur. Many are photosynthetic, while others are heterotrophic.	Armoured forms have stiff cellulose plates. Motile stages typically possess two flagella: one longitudinal and the other transverse in a furrow.	Blooms arising from rapid multiplication of some Gonyaulax species can colour seawater red (red tides). Toxin-producing blooms can harm or kill marine animals; red coloration alone does not establish toxicity.
Euglenoids	Found in stagnant freshwater; some mixotrophic members, including some Euglena species, can photosynthesise in sunlight and feed heterotrophically.	A protein layer called the pellicle makes the body flexible.	Euglena.
Protozoans	Free-living and parasitic heterotrophs.	Four major groups: amoeboid, flagellated, ciliated and sporozoan.	Examples and disease associations are compared below.
Slime moulds	Plasmodial slime moulds chiefly feed by phagocytosis, ingesting bacteria and other microorganisms. They grow on decaying twigs and leaves.	Under suitable conditions, plasmodial slime moulds grow as a plasmodium, a multinucleate mass of protoplasm; under unfavourable conditions, it differentiates into fruiting bodies bearing spores at their tips.	Ectoplasm and nuclei are features of the plasmodium.

Illustrated scheme of a diatom shell with two overlapping halves. — A diatom shell has two overlapping halves, fitting together like a soap box.

Coloured dinoflagellate diagram with a plated surface and transverse and longitudinal flagella. — An armoured dinoflagellate: cellulose plates and two differently oriented flagella.

Apical pore: a pore at the apex of the dinoflagellate.
Cingulum: the transverse girdle or furrow associated with the transverse flagellum.
Dinoflagellates can possess trichocysts.

Some mixotrophic euglenoids, including some Euglena species, can photosynthesise in sunlight; when sunlight is unavailable and organic food is available, these organisms can feed heterotrophically. This combination of nutritional modes is called mixotrophic nutrition.

Coloured illustration of an elongated Euglena with a flagellum, green chloroplasts, a nucleus and a red eyespot. — Euglena is a euglenoid with a flexible pellicle and a flagellum.

Euglena has a nucleus, flagellum, photoreceptor and contractile vacuole.
Ciliated protozoans such as Paramecium use cilia for locomotion and to move food into a gullet.

Four groups of protozoans

Group	Defining feature	Examples and associations
Amoeboid	Catch prey using pseudopodia.	Examples include Amoeba and Entamoeba; Entamoeba includes parasitic forms.
Flagellated	Have one or more flagella.	Trypanosoma causes sleeping sickness.
Ciliated	Cilia move food into the gullet and help in locomotion.	Paramecium.
Sporozoan	Have an infective spore-like stage in the life cycle.	Plasmodium causes malaria.

Labelled Paramecium diagram showing cilia, an oral groove, micronucleus, macronucleus, cytoplasm and contractile vacuoles, including one near the anterior end. — Paramecium uses cilia for movement and to direct food toward its mouth and into the gullet (cytopharynx). Its cytoplasm contains a micronucleus and contractile vacuoles, including an anterior contractile vacuole.

Slime-mould spores have true walls that are highly resistant. The spores can survive for many years and are dispersed by air currents.

Coloured schematic of a plasmodial slime mould life cycle, including a multinucleate plasmodium, sporangia and spores. — A plasmodial slime mould forms a multinucleate plasmodium and spore-bearing fruiting bodies.

Kingdom Fungi

Fungal reproduction
- Vegetative reproduction
  - Fragmentation
  - Fission
  - Budding
- Asexual reproduction
  - Conidia
  - Sporangiospores
  - Zoospores
- Examples of sexual spores
  - Ascospores
    In true fungi.
  - Basidiospores
    In true fungi.
  - Oospores
    In oomycetes, included with fungi in older classifications.

Fungal reproduction

Vegetative reproduction
- Fragmentation
- Fission
- Budding
Asexual reproduction
- Conidia
- Sporangiospores
- Zoospores
Examples of sexual spores
- Ascospores
  In true fungi.
- Basidiospores
  In true fungi.
- Oospores
  In oomycetes, included with fungi in older classifications.

Fungal reproduction includes a sexual cycle.

Comparison of fungal groups

Mucor mycelium bearing dark sporangia. — Mucor

Three upright stalks bear spore-filled sporangia above a network of hyphae. — Sporangia in a mould

Group	Habitat or nutrition	Mycelium	Vegetative and asexual reproduction	Sexual reproduction	Examples
Phycomycetes — historical grouping	Aquatic habitats and decaying wood in moist, damp places.	Aseptate and coenocytic.	Zoospores (motile) or aplanospores (non-motile).		Mucor, Rhizopus and Albugo.
Ascomycetes — sac fungi	Saprophytic decomposers, parasitic or coprophilous (growing on dung).	Branched and septate.	Asexual spores are conidia.	Sexual spores called ascospores form within asci. In many filamentous ascomycetes, asci occur in fruiting bodies called ascocarps.	Neurospora, Aspergillus and Claviceps.
Basidiomycetes — club fungi		Branched and septate.	Vegetative reproduction occurs by fragmentation; asexual spores are generally uncommon.	Sexual reproduction commonly begins with fusion of compatible vegetative or somatic cells. Basidia form subsequently; nuclear fusion and meiosis in them lead to basidiospore formation.	Agaricus, Ustilago and Puccinia.
Deuteromycetes — historical grouping (fungi imperfecti)	Some members are saprophytes or parasites.	Branched and septate.	Members were grouped here when only their vegetative and asexual phases were known.		Alternaria, Trichoderma and Colletotrichum.

Schematic drawing of Rhizopus showing sporangia on upright stalks, with a connecting stolon and branching rhizoids. — Rhizopus: spore cases are supported on upright stalks above the branching mycelium.

Static coloured illustration of a button mushroom, Agaricus bisporus, with a cap and stalk. — Agaricus has a mushroom fruiting body with a cap and stalk.

Ascomycete reproductive structures
- Ascocarp
  Contains asci in many filamentous forms.
  - Asci
    Ascospores
    Sexual spores formed inside asci.
- Conidia
  Asexual spores.

Ascomycete reproductive structures

Ascocarp
Contains asci in many filamentous forms.
- Asci
  - Ascospores
    Sexual spores formed inside asci.
Conidia
Asexual spores.

An ascocarp holds elongated asci containing ascospores. — Ascocarp and asci

A coenocytic hypha

Rhizopus hypha
- Hyphal exterior
  - Hyphal wall
- Hyphal tip
- Hyphal interior
  - Cytoplasm
  - Multiple nuclei
  - Oil drops

Aseptate, multinucleate (coenocytic).

Rhizopus hypha

Aseptate, multinucleate (coenocytic).

Hyphal exterior
- Hyphal wall
Hyphal tip
Hyphal interior
- Cytoplasm
- Multiple nuclei
- Oil drops

Static illustration of a branching network of fungal filaments. — Branching fungal hyphae form a mycelium. The accompanying structure diagram describes the wall, cytoplasm, nuclei and oil droplets of a coenocytic Rhizopus hypha.

Viruses

Viruses are non-cellular obligate parasites that take over the machinery of a host cell on entering it.

Viruses depend on host cells for replication and are metabolically inactive outside them, making their living status difficult to assign.

Particular viruses, including tobacco mosaic virus, can be crystallised; crystallinity is not their general extracellular state.

Viruses present a challenge for biological classification.

Names and observations

“Virus” is a Latin word meaning venom or poisonous fluid; it predates Pasteur.
D. J. Ivanovsky found that certain microbes caused tobacco mosaic disease in tobacco plants.
M. W. Beijerinck called the fluid Contagium vivum fluidum because extracts from infected tobacco plants could infect healthy plants.
W. M. Stanley crystallised tobacco mosaic virus, whose particles contain protein and RNA and remain inactive outside a suitable host.

Viroids, prions and lichens

A loop represents a circular viroid RNA molecule. Folded strands represent a misfolded prion protein. — A viroid and a prion

Agent	Composition and properties	Disease associations	Other properties
Viroids	Infectious free RNA of low molecular weight; lacks a protein coat.	Potato spindle tuber disease.	Discovered by T. O. Diener.
Prions	Infectious agents consisting of abnormally folded protein, associated with transmission of certain neurological diseases.	Prions cause bovine spongiform encephalopathy (BSE), or mad cow disease, in cattle and Creutzfeldt-Jakob disease (CJD) in humans. The human form specifically associated with BSE is variant CJD (vCJD).	Prion proteins can form aggregates of varying sizes; they have no single particle size comparable to viruses.

Lichens: a symbiotic association

Phycobiont — algal partner

Provides food in the symbiotic association.

Mycobiont — fungal partner

Provides shelter and absorbs nutrients and water for the alga.

Unnumbered illustrated lichen cross-section, with green algal cells embedded among branching fungal hyphae. — In this lichen cross-section, green algal cells sit among branching fungal hyphae.

Many lichens are sensitive to air pollution, so their presence, absence and community composition can indicate air quality.

Kingdom

Organisation

Nutrition and reserves

Distinguishing features

Monera

Prokaryotic; bacteria are its sole members.

Photosynthetic autotrophs, chemosynthetic autotrophs or heterotrophs.

Bacteria occur almost everywhere.

Protista

Primarily unicellular eukaryotes.

Variable nutrition.

Forms a link between plants, animals and fungi.

Fungi

Eukaryotic; mostly multicellular.

Heterotrophic by absorption; saprophytic, parasitic or symbiotic. Reserve food: glycogen.

Achlorophyllous, spore-forming and non-vascular. True fungal walls contain chitin and glucans; some cellulose-walled organisms were included with fungi in older classifications.

Animalia

Multicellular and eukaryotic; cell walls are absent.

Non-green heterotrophs; holozoic nutrition by ingestion. Reserve food: glycogen or fats.

Sexual reproduction involves gamete fusion followed by embryological development; copulation occurs in some groups.

Plantae

Eukaryotic and mostly multicellular; most plants bear chlorophyll.

Most plants are green and photosynthetic; nonphotosynthetic exceptions occur.

Includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms.

Nutritional group

Features and examples

Photosynthetic autotrophs

Cyanobacteria, also called blue-green algae (BGA). Some, such as Anabaena and Nostoc, have specialised cells called heterocysts for nitrogen fixation.

Chemosynthetic autotrophs

Oxidise inorganic substrates such as nitrite and ammonia, using the released energy for ATP production. They help recycle N, P, Fe and S.

Heterotrophic bacteria

Include decomposers and bacteria involved in curd-making, antibiotic production and N₂ fixation. Other heterotrophic bacteria cause diseases such as typhoid, tetanus and citrus canker.

Group

Habitat and nutrition

Structure and behaviour

Examples and significance

Chrysophytes

Freshwater or marine; photosynthetic microscopic plankton.

In diatoms, silica-rich cell walls resist decay; their two overlapping halves fit together like a soap box.

In this historical grouping, chrysophytes include diatoms, golden algae and desmids; desmids are green algae, distinct from golden algae. Accumulated diatom walls form diatomaceous material used for polishing and filtration of oils and syrups.

Dinoflagellates

Most are marine; freshwater forms also occur. Many are photosynthetic, while others are heterotrophic.

Armoured forms have stiff cellulose plates. Motile stages typically possess two flagella: one longitudinal and the other transverse in a furrow.

Blooms arising from rapid multiplication of some Gonyaulax species can colour seawater red (red tides). Toxin-producing blooms can harm or kill marine animals; red coloration alone does not establish toxicity.

Euglenoids

Found in stagnant freshwater; some mixotrophic members, including some Euglena species, can photosynthesise in sunlight and feed heterotrophically.

A protein layer called the pellicle makes the body flexible.

Euglena.

Protozoans

Free-living and parasitic heterotrophs.

Four major groups: amoeboid, flagellated, ciliated and sporozoan.

Examples and disease associations are compared below.

Slime moulds

Plasmodial slime moulds chiefly feed by phagocytosis, ingesting bacteria and other microorganisms. They grow on decaying twigs and leaves.

Under suitable conditions, plasmodial slime moulds grow as a plasmodium, a multinucleate mass of protoplasm; under unfavourable conditions, it differentiates into fruiting bodies bearing spores at their tips.

Ectoplasm and nuclei are features of the plasmodium.

Group

Defining feature

Examples and associations

Amoeboid

Catch prey using pseudopodia.

Examples include Amoeba and Entamoeba; Entamoeba includes parasitic forms.

Flagellated

Have one or more flagella.

Trypanosoma causes sleeping sickness.

Ciliated

Cilia move food into the gullet and help in locomotion.

Paramecium.

Sporozoan

Have an infective spore-like stage in the life cycle.

Plasmodium causes malaria.

Group

Habitat or nutrition

Mycelium

Vegetative and asexual reproduction

Sexual reproduction

Examples

Phycomycetes — historical grouping

Aquatic habitats and decaying wood in moist, damp places.

Aseptate and coenocytic.

Zoospores (motile) or aplanospores (non-motile).

Mucor, Rhizopus and Albugo.

Ascomycetes — sac fungi

Saprophytic decomposers, parasitic or coprophilous (growing on dung).

Branched and septate.

Asexual spores are conidia.

Sexual spores called ascospores form within asci. In many filamentous ascomycetes, asci occur in fruiting bodies called ascocarps.

Neurospora, Aspergillus and Claviceps.

Basidiomycetes — club fungi

Branched and septate.

Vegetative reproduction occurs by fragmentation; asexual spores are generally uncommon.

Sexual reproduction commonly begins with fusion of compatible vegetative or somatic cells. Basidia form subsequently; nuclear fusion and meiosis in them lead to basidiospore formation.

Agaricus, Ustilago and Puccinia.

Deuteromycetes — historical grouping (fungi imperfecti)

Some members are saprophytes or parasites.

Branched and septate.

Members were grouped here when only their vegetative and asexual phases were known.

Alternaria, Trichoderma and Colletotrichum.

Agent

Composition and properties

Disease associations

Other properties

Viroids

Infectious free RNA of low molecular weight; lacks a protein coat.

Potato spindle tuber disease.

Discovered by T. O. Diener.

Prions

Infectious agents consisting of abnormally folded protein, associated with transmission of certain neurological diseases.

Prions cause bovine spongiform encephalopathy (BSE), or mad cow disease, in cattle and Creutzfeldt-Jakob disease (CJD) in humans. The human form specifically associated with BSE is variant CJD (vCJD).

Prion proteins can form aggregates of varying sizes; they have no single particle size comparable to viruses.

Revisions

Biological Classification

Relationships in the historical five-kingdom model