Chapter-2: Biological Classification

Five Kingdom Classification

Biological classification is the scientific process of arranging organisms into groups and subgroups based on similarities and differences. Over time, classification systems have evolved from simple two-kingdom systems to more comprehensive multi-kingdom models that better reflect evolutionary relationships.

Historical Context and Evolution

Initially, Aristotle used simple morphological characters to classify plants into trees, shrubs, and herbs, and animals into two groups: those with red blood and those without. Later, the Two Kingdom classification was developed by Linnaeus, dividing all living things into Plantae and Animalia.

Limitations of the Two Kingdom System

While simple, the two-kingdom system had severe drawbacks:

• It did not distinguish between eukaryotes and prokaryotes.
• It grouped unicellular and multicellular organisms together (e.g., Chlamydomonas and Spirogyra placed under algae in plants).
• It failed to differentiate between photosynthetic organisms (green algae/plants) and non-photosynthetic organisms (fungi), even though fungi have chitin in their cell walls unlike plants which have cellulose.

Introduction of the Five Kingdom System

To overcome these limitations, R.H. Whittaker (1969) proposed the Five Kingdom Classification. The kingdoms defined by him were Monera, Protista, Fungi, Plantae, and Animalia.

Criteria for Five Kingdom Classification

Whittaker used five primary criteria to classify organisms:

1. Cell structure: Whether the organism is prokaryotic or eukaryotic.
2. Thallus organization: Whether the body is unicellular or multicellular.
3. Mode of nutrition: Autotrophic (photosynthetic/chemosynthetic) vs. Heterotrophic (absorptive/ingestive).
4. Reproduction: Sexual and asexual methods.
5. Phylogenetic relationships: Evolutionary history and descent.

Monera

Kingdom Monera includes all prokaryotic organisms. Bacteria are the sole members of Kingdom Monera and are the most abundant micro-organisms found almost everywhere.

Salient Features of Monera

• They are prokaryotic, meaning they lack a true membrane-bound nucleus and membrane-bound organelles.
• Their genetic material is a naked, circular DNA strand known as the nucleoid.
• Ribosomes are of the 70S type.
• Cell walls are generally present, composed of peptidoglycan.
• They show the most extensive metabolic diversity.

Classification of Bacteria Based on Shape

Bacteria are grouped under four categories based on their basic shapes:

• Coccus (plural: Cocci): Spherical shape. Example: Pneumococcus.
• Bacillus (plural: Bacilli): Rod-shaped. Example: Lactobacillus.
• Spirillum (plural: Spirilla): Spiral shape. Example: Spirillum.
• Vibrio: Comma-shaped. Example: Vibrio cholerae.

Major Groups within Kingdom Monera

Kingdom Monera is broadly divided into Archaebacteria and Eubacteria.

1. Archaebacteria

Archaebacteria are special because they live in some of the most harsh habitats, such as extreme salty areas (halophiles), hot springs (thermoacidophiles), and marshy areas (methanogens). They survive extreme conditions due to a different cell wall structure than other bacteria.

• Methanogens: Present in the guts of several ruminant animals (like cows and buffaloes) and responsible for the production of methane (biogas) from the dung of these animals.

2. Eubacteria (True Bacteria)

Eubacteria are characterized by the presence of a rigid cell wall and, if motile, a flagellum.

• Cyanobacteria: Also referred to as blue-green algae. They have chlorophyll a similar to green plants and are photosynthetic autotrophs. They can be unicellular, colonial, or filamentous, freshwater/marine or terrestrial. Their colonies are generally surrounded by a gelatinous sheath. Some of these organisms can fix atmospheric nitrogen in specialized cells called heterocysts (e.g., Nostoc and Anabaena).
• Chemosynthetic Autotrophic Bacteria: Oxidize various inorganic substances such as nitrates, nitrites, and ammonia and use the released energy for ATP production. They play a great role in recycling nutrients like nitrogen, phosphorous, iron, and sulphur.
• Heterotrophic Bacteria: The most abundant in nature. The majority are important decomposers. Many are helpful to human beings: making curd from milk, production of antibiotics, and fixing nitrogen in legume roots. Some are pathogens causing diseases like cholera, typhoid, tetanus, and citrus canker.

Reproduction in Bacteria

Bacteria mainly reproduce by fission. Under unfavorable conditions, they produce spores. They also reproduce by a sort of sexual reproduction by adopting a primitive type of DNA transfer from one bacterium to the other (conjugation, transformation, transduction).

Mycoplasma

Mycoplasmas are organisms that completely lack a cell wall. They are the smallest living cells known and can survive without oxygen. Many mycoplasmas are pathogenic in animals and plants.

Protista

All single-celled eukaryotes are placed under Protista, but the boundaries of this kingdom are not well defined. It forms a connecting link with plants, animals, and fungi.

Salient Features of Protista

• They are unicellular eukaryotes.
• Being eukaryotes, the cell body contains a well-defined nucleus and membrane-bound organelles.
• Some have flagella or cilia for locomotion.
• Reproduction is asexual (cell division, spore formation) and sexual (zygote formation by cell fusion).

Major Groups of Protista

Kingdom Protista is classified into five major groups:

1. Chrysophytes

This group includes diatoms and golden algae (desmids). They are found in fresh water as well as marine environments. They are microscopic and float passively in water currents (plankton).

• Most of them are photosynthetic.
• In diatoms, the cell walls form two thin overlapping shells, which fit together as in a soap box.
• The walls are embedded with silica and thus the walls are indestructible. Thus, diatoms have left behind large amounts of cell wall deposits in their habitat; this accumulation over billions of years is referred to as diatomaceous earth.
• Being gritty, this soil is used in polishing, filtration of oils and syrups. Diatoms are the chief producers in the oceans.

2. Dinoflagellates

These organisms are mostly marine and photosynthetic. They appear yellow, green, brown, blue, or red depending on the main pigments present in their cells.

• The cell wall has stiff cellulose plates on the outer surface.
• Most of them have two flagella; one lies longitudinally and the other transversely in a furrow between the wall plates.
• Very often, red dinoflagellates (Example: Gonyaulax) undergo such rapid multiplication that they make the sea appear red (red tides). Toxins released by such large numbers may even kill other marine animals such as fishes.

3. Euglenoids

These are freshwater organisms found in stagnant water. Instead of a cell wall, they have a protein-rich layer called a pellicle which makes their body flexible.

• They have two flagella, a short and a long one.
• Although they are photosynthetic in the presence of sunlight, when deprived of sunlight they behave like heterotrophs by predating on other smaller organisms.
• Interestingly, the pigments of euglenoids are identical to those present in higher plants. Example: Euglena.

4. Slime Moulds

Slime moulds are saprophytic protists. The body moves along decaying twigs and leaves engulfing organic material.

• Under suitable conditions, they form an aggregation called plasmodium which may grow and spread over several feet.
• During unfavourable conditions, the plasmodium differentiates and fruiting bodies bearing spores at their tips are formed.
• The spores possess true walls and are extremely resistant, surviving for many years, even under adverse conditions.

5. Protozoans

All protozoans are heterotrophs and live as predators or parasites. They are believed to be primitive relatives of animals. They are divided into four major groups:

• Amoeboid protozoans: Live in fresh water, sea water, or moist soil. They move and capture their prey by putting out pseudopodia (false feet) as in Amoeba. Marine forms have silica shells on their surface. Some are parasites like Entamoeba.
• Flagellated protozoans: The members of this group are either free-living or parasitic. They have flagella. Parasitic forms cause diseases such as sleeping sickness. Example: Trypanosoma.
• Ciliated protozoans: These are aquatic, actively moving organisms because of the presence of thousands of cilia. They have a cavity (gullet) that opens to the outside of the cell surface. The coordinated movement of rows of cilia causes water laden with food to be steered into the gullet. Example: Paramoecium.
• Sporozoans: This group includes diverse organisms that have an infectious spore-like stage in their life cycle. The most notorious is Plasmodium (malarial parasite) which causes malaria, a disease which has a staggering effect on human population.

Fungi

Fungi constitute a unique kingdom of heterotrophic organisms. They show a great diversity in morphology and habitat.

Salient Features of Fungi

• Fungi are cosmopolitan and occur in air, water, soil, and on animals and plants.
• They prefer to grow in warm and humid places.
• With the exception of yeasts (which are unicellular), fungi are filamentous.
• Their bodies consist of long, slender thread-like structures called hyphae. The network of hyphae is known as mycelium.
• Hyphae are either continuous tubes filled with multinucleated cytoplasm (coenocytic hyphae) or they have septae or cross walls (septate hyphae).
• The cell walls of fungi are composed of chitin and polysaccharides.

Nutrition in Fungi

Most fungi are heterotrophic and absorb organic matter from dead substrates and are hence called saprophytes. Those that depend on living plants and animals are called parasites. They can also live as symbionts in association with algae as lichens and with roots of higher plants as mycorrhiza.

Reproduction in Fungi

Reproduction in fungi can take place by vegetative means (fragmentation, fission, and budding), asexual reproduction (by spores called conidia or sporangiospores or zoospores), and sexual reproduction (by oospores, ascospores, and basidiospores).

The sexual cycle involves three steps:

1. Fusion of protoplasms between two motile or non-motile gametes called plasmogamy.
2. Fusion of two nuclei called karyogamy.
3. Meiosis in zygote resulting in haploid spores.

When a fungus reproduces sexually, two haploid hyphae of compatible mating types come together and fuse. In some fungi, the fusion of two haploid cells immediately results in diploid cells (2n). However, in other fungi (ascomycetes and basidiomycetes), an intervening dikaryotic stage occurs (n + n, i.e., two nuclei per cell); such a condition is called a dikaryon and the phase is called the dikaryophase. Later, parental nuclei fuse and the cells become diploid.

Classification of Fungi

The morphology of the mycelium, mode of spore formation, and fruiting bodies form the basis for the division of the kingdom into various classes:

1. Phycomycetes

Habit and Habitat: Found in aquatic habitats and on decaying wood in moist and damp places or as obligate parasites on plants.

Mycelium: Aseptate and coenocytic.

Reproduction: Asexual reproduction takes place by zoospores (motile) or by aplanospores (non-motile). These spores are endogenous inside the sporangium. Zygospores are formed by fusion of two gametes.

Examples: Mucor, Rhizopus (the bread mould), and Albugo (the parasitic fungi on mustard).

2. Ascomycetes (Sac Fungi)

Habit and Habitat: Mostly multicellular, rarely unicellular (e.g., yeast, Saccharomyces). Saprophytic, decomposers, parasitic, or coprophilous (growing on dung).

Mycelium: Branched and septate.

Reproduction: Asexual reproduction is by conidia produced exogenously on the special mycelium called conidiophores. Sexual reproduction is by ascospores produced endogenously in sac like asci (singular: ascus). These asci are arranged in different types of fruiting bodies called ascocarps.

Examples: Aspergillus, Claviceps, Neurospora (extensively used in biochemical and genetic work), morels, and truffles (edible and considered delicacies).

3. Basidiomycetes (Club Fungi)

Habit and Habitat: Commonly known forms are mushrooms, bracket fungi, or puffballs. They grow in soil, on logs and tree stumps, and in living plant bodies as parasites (rusts and smuts).

Mycelium: Branched and septate.

Reproduction: Asexual spores are generally not found, but vegetative reproduction by fragmentation is common. Plasmogamy is brought about by fusion of two vegetative or somatic cells of different strains or genotypes. The resultant structure is dikaryotic which ultimately gives rise to basidium. Karyogamy and meiosis take place in the basidium producing four basidiospores. The basidiospores are exogenously produced on the basidium. The basidia are arranged in fruiting bodies called basidiocarps.

Examples: Agaricus (mushroom), Ustilago (smut), and Puccinia (rust fungus).

4. Deuteromycetes (Fungi Imperfecti)

Habit and Habitat: Commonly known as imperfect fungi because only their asexual or vegetative phases are known. When the sexual forms of these fungi were discovered they were moved into classes they rightly belong to (ascomycetes or basidiomycetes).

Mycelium: Septate and branched.

Reproduction: Reproduce only by asexual spores known as conidia.

Examples: Alternaria, Colletotrichum, and Trichoderma.

Lichens, Viruses, Viroids, and Prions

In the five-kingdom classification of Whittaker, there is no mention of lichens and some acellular organisms like viruses, viroids, and prions. These are briefly described below:

Lichens

Lichens are symbiotic associations mutually useful organisms between algae and fungi.

• The algal component is known as phycobiont (autotrophic) and fungal component is mycobiont (heterotrophic).
• Algae prepare food for fungi and fungi provide shelter and absorb mineral nutrients and water for its partner.
• Lichens are very good pollution indicators as they do not grow in polluted areas.

Viruses

Viruses are non-cellular organisms that are characterized by having an inert crystalline structure outside the living cell.

• Once they infect a cell they take over the machinery of the host cell to replicate themselves, killing the host.
• The name virus that means venom or poisonous fluid was given by Pasteur. D.J. Ivanowsky recognized certain microbes as causal agent of the mosaic disease of tobacco.
• W.M. Stanley showed that viruses could be crystallized and crystals consist largely of proteins.
• In addition to proteins, viruses also contain genetic material, that could be either RNA or DNA. No virus contains both RNA and DNA.
• A virus is a nucleoprotein and the genetic material is infectious.
• In general, viruses that infect plants have single-stranded RNA and viruses that infect animals have either single or double-stranded RNA or double-stranded DNA.
• Bacterial viruses or bacteriophages are usually double-stranded DNA viruses.
• The protein coat called capsid made of small subunits called capsomeres, protects nucleic acid.
• Viruses cause diseases like mumps, smallpox, herpes, influenza, and AIDS. In plants, the symptoms can be mosaic formation, leaf rolling and curling, yellowing and vein clearing, dwarfing, and stunted growth.

Viroids

In 1971 T.O. Diener discovered a new infectious agent that was smaller than viruses and caused potato spindle tuber disease.

• It was found to be a free RNA; it lacked the protein coat that is found in viruses, hence the name viroid.
• The RNA of the viroid was of low molecular weight.

Prions

In modern medicine certain infectious neurological diseases were found to be transmitted by an agent consisting of abnormally folded protein.

• The agent was similar in size to viruses. These agents were called prions.
• The most notable diseases caused by prions are bovine spongiform encephalopathy (BSE) commonly called mad cow disease in cattle and its analogous variant Creutzfeldt-Jakob disease (CJD) in humans.