CHAPTER - 2 BIOLOGICAL CLASSIFICATION

Topic Covered ✏

2.1 Kingdom Monera 
2.2 Kingdom Protista 
2.3 Kingdom Fungi 
2.4 Kingdom Plantae 
2.5 Kingdom Animalia 
2.6 Viruses, Viroids and Lichens

Introduction 

• Aristotle was the earliest to attempt a more scientific basis for classification. 
• He used simple morphological characters to classify plants into trees, shrubs and herbs. 
• He also divided animals into two groups, those which had red blood and those that did not.

Two Kingdom

• Given by Linnaeus' ( Plantae and Animalia )
• This system did not distinguish between the :-

• Eukaryotes and prokaryotes, 
• Unicellular and multicellular organisms and 
• Photosynthetic (green algae) and non-photosynthetic (fungi) organisms.

Five Kingdom Classification.

• Proposed by R.H. Whittaker (1969) 
• The kingdoms defined by him were named Monera, Protista, Fungi, Plantae and Animalia. 
• The main criteria for classification used by him include
• Cell structure, 
• Body organisation, 
• Mode of nutrition, 
• Reproduction and 
• Phylogenetic relationships.

Three-domain system/ six kingdom classification. 

• Given by Carl woese, based on 16s rRNA.
• He divides the Kingdom Monera into two domains, leaving the remaining eukaryotic kingdoms in the third domain.

• Earlier classification systems included bacteria, blue green algae, fungi, mosses, ferns, gymnosperms and the angiosperms under ‘Plants’. The character that unified this whole kingdom was that all the organisms included had a cell wall in their cells.
• According to Five kingdom classification, Kingdom Protista has brought together Chlamydomonas, Chlorella (earlier placed in Algae within Plants and both having cell walls) with Paramoecium and Amoeba (which were earlier placed in the animal kingdom which lack cell wall).

2.1 Kingdom Monera 

• Bacteria are the sole members of the Kingdom Monera. 
• They are the most abundant micro-organisms. 
• Bacteria occur almost everywhere. Hundreds of bacteria are present in a handful of soil. They also live in extreme habitats such as hot springs, deserts, snow and deep oceans where very few other life forms can survive. 
• Many of them live in or on other organisms as parasites. 

• Bacteria are grouped under four categories based on their shape: 
• Spherical (Coccus)
• Rod-shaped (Bacillus)
• Comma-shaped (Vibrium)
• Spiral-shaped (Spirillum)

    Body organisation

• Though the bacterial structure is very simple, they are very complex in behaviour. 
• Compared to many other organisms, bacteria as a group show the most extensive metabolic diversity. 

    Nutrition

• Some of the bacteria are autotrophic, i.e., they synthesise their own food from inorganic substrates. They may be photosynthetic autotrophic or chemosynthetic autotrophic. 
• The vast majority of bacteria are heterotrophs, i.e., they depend on other organisms or on dead organic matter for food.

2.1.1 Archaebacteria

• These bacteria are special since they live in some of the most harsh habitats such as 

1. Extreme salty areas (halophiles), 
2. Hot springs (thermoacidophiles) and 
3. Marshy areas (methanogens). 

• Archaebacteria differ from other bacteria in having a different cell wall structure and this feature is responsible for their survival in extreme conditions. 
• Methanogens are present in the gut of several ruminant animals such as cows and buffaloes and they are responsible for the production of methane (biogas) from the dung.

2.1.2 Eubacteria 

• There are thousands of different eubacteria or ‘true bacteria’. 
• They are characterised by the presence of a rigid cell wall, and if motile, a flagellum. 

A. Photosynthetic autotrophic

    Cyanobacteria 

• The cyanobacteria (also referred to as blue-green algae) have chlorophyll a similar to green plants and are photosynthetic autotrophs.
• The cyanobacteria are unicellular, colonial or filamentous, freshwater/marine or terrestrial algae. 
• The colonies are generally surrounded by gelatinous sheath. They often form blooms in polluted water bodies. 
• Some of these organisms can fix atmospheric nitrogen in specialised cells called heterocysts, e.g., Nostoc and Anabaena. 

B. Chemosynthetic autotrophic 

• These bacteria oxidise various inorganic substances such as nitrates, nitrites and ammonia and use the released energy for their ATP production. 
• They play a great role in recycling nutrients like nitrogen, phosphorous, iron and sulphur. 

C. Heterotrophic bacteria

• Heterotrophic bacteria are most abundant in nature. 
• The majority are important decomposers. 
• Many of them have a significant impact on human affairs. 
• They are helpful in making curd from milk, production of antibiotics, fixing nitrogen in legume roots, etc. 
• Some are pathogens causing damage to human beings, crops, farm animals and pets. 
• Cholera, typhoid, tetanus, citrus canker are well known diseases caused by different bacteria. 

Reproduction in bacteria

      1. Bacteria reproduce mainly by fission . 

                 

      2. Sometimes, under unfavourable conditions, they produce spores. 
      3. They also reproduce by a sort of sexual reproduction by adopting a primitive type 

          of  DNA transfer from one bacterium to the other. 

Mycoplasma 

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

2.2 Kingdom Protista 

• All single-celled eukaryotes are placed under Protista, but the boundaries of this kingdom are not well defined. 
• Members of Protista are primarily aquatic. This kingdom forms a link with the others dealing with plants, animals and fungi. 
• Some have flagella or cilia. 

Reproduction in protista

1. Asexually and 
2. Sexually by a process involving cell fusion and zygote formation.

Kingdom Protista divided into 5 groups :-

2.2.1 Chrysophytes 

• This group includes diatoms and golden algae (desmids). 
• They are microscopic and float passively in water currents (plankton). 
• 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 amount 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. 

2.2.2 Dinoflagellates

• 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.

2.2.3 Euglenoids 

• Instead of a cell wall, they have a protein rich layer called pellicle which makes their body flexible. 
• They have two flagella, a short and a long one. 
• 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 

2.2.4 Slime Moulds 

• 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 forms fruiting bodies bearing spores at their tips. 
• The spores possess true walls. They are extremely resistant and survive for many years, even under adverse conditions. 
• The spores are dispersed by air currents.

2.2.5 Protozoans 

• All protozoans are heterotrophs and live as predators or parasites. 
• They are believed to be primitive relatives of animals. 

There are four major groups of protozoans :-

     A.  Amoeboid protozoans: 

• These organisms 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 of them such as Entamoeba are parasites. 

     B.  Flagellated protozoans: 

• The members of this group are either free-living or parasitic. 
• They have flagella. 
• The parasitic forms cause diaseases such as sleeping sickness. 
• Example: Trypanosoma. 

     C.  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 the water laden with food to be steered into the gullet. 
• Example: Paramoecium 

     D.  Sporozoans: 

• This 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.

2.3 KINGDOM FUNGI 

• The fungi constitute a unique kingdom of heterotrophic organisms. 
• They show a great diversity in morphology and habitat. 
• The common mushroom you eat and toadstools are also fungi. 
• Some unicellular fungi, e.g., yeast are used to make bread and beer. 

• Wheat rust-causing Puccinia
• Some are the source of antibiotics, e.g., Penicillium. 

Habitat

• Fungi are cosmopolitan and occur in air, water, soil and on animals and plants. 
• They prefer to grow in warm and humid places.  

Body Organisation

• With the exception of yeasts which are unicellular, fungi are filamentous. 
• The cell walls of fungi are composed of chitin and polysaccharides. 
• Their bodies consist of long, slender thread-like structures called hyphae. 
• The network of hyphae is known as mycelium. 
• Some hyphae are continuous tubes filled with multinucleated cytoplasm – these are called coenocytic hyphae. 
• Others have septae or cross walls in their hyphae. 

Nutrition

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

Reproduction

• Vegetative means – fragmentation, fission and budding. 
• Asexual reproduction – by sporescalled conidia or sporangiospores or zoospores.
• Sexual reproduction – by oospores, ascospores and basidiospores. 
• The various spores are produced in distinct structures called fruiting bodies. 
• The sexual cycle involves the following three steps: 

1. Plasmogamy - Fusion of protoplasms between two motile or non-motile gametes
2. Karyogamy - 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). 
• In other fungi (ascomycetes and basidiomycetes), an intervening  dikaryotic stage  (n + n, i.e., two nuclei per cell) occurs; such a condition is called a dikaryon and the phase is called dikaryophase of fungus. Later, the parental nuclei fuse and the cells become diploid. 
• The fungi form fruiting bodies in which reduction division occurs, leading to formation of haploid spores. 
• The morphology of the mycelium, mode of spore formation and fruiting bodies form the basis for the division of the kingdom into various classes.

KINGDOM FUNGI divided into 4 Classes :-

2.3.1 Phycomycetes 

• Members of phycomycetes are found in aquatic habitats and on decaying wood in moist and damp places or as obligate parasites on plants. 
• Asexual reproduction - takes place by 
• Zoospores (motile) or 
• Aplanospores (non-motile). 

These spores are endogenously produced in sporangium. 

• Sexual reproduction - 
• A zygospore is formed by fusion of two gametes. 
• These gametes are similar in morphology (isogamous) or dissimilar (anisogamous or oogamous). 
• Some common examples are 
• Mucor 
• Rhizopus (the bread mould mentioned earlier) and 
• Albugo (the parasitic fungi on mustard).

2.3.2 Ascomycetes 

• Commonly known as sac-fungi, 
• The ascomycetes are mostly multicellular, e.g., Penicillium, or rarely unicellular, e.g., yeast (Saccharomyces). 
• They are saprophytic, decomposers, parasitic or coprophilous (growing on dung). 
• Asexual reproduction - 
• The asexual spores are conidia produced exogenously on the special mycelium called conidiophores. 
• Conidia on germination produce mycelium. 
• Sexual reproduction - 
• Sexual spores are called ascospores which are produced endogenously in sac like asci (singular ascus). 
• These asci are arranged in different types of fruiting bodies called ascocarps. 

• Examples are 
• Aspergillus 
• Claviceps and 
• Neurospora. 
• Morels and truffles

• Neurospora is used extensively in biochemical and genetic work. 
• Many members like morels and truffles are edible and are considered delicacies. 

2.3.3 Basidiomycetes 

• Commonly known forms of basidiomycetes are mushrooms, bracket fungi or puffballs. 
• They grow in soil, on logs and tree stumps and in living plant bodies as parasites, e.g., rusts and smuts. 
• Asexual reproduction - 
• The asexual spores are generally not found, but vegetative reproduction by fragmentation is common. 
• Sexual reproduction - 
• The sex organs are absent, but 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 are 
• Agaricus (mushroom) 
• Ustilago (smut) and 
• Puccinia (rust fungus).

2.3.4 Deuteromycetes 

• Commonly known as imperfect fungi because only the asexual or vegetative phases of these fungi are known. 
• The deuteromycetes reproduce only by asexual spores known as conidia. 
• Once perfect (sexual) stages of members of dueteromycetes were discovered they were often moved to ascomycyetes and basidiomycetes. 
• Some members are saprophytes or parasites while a large number of them are decomposers of litter and help in mineral cycling. 
• Examples are 
• Alternaria, 
• Colletotrichum and 
• Trichoderma. 

2.4 KINGDOM PLANTAE

• Includes all eukaryotic chlorophyll-containing organisms commonly called plants. 
• A few members are partially heterotrophic such as the insectivorous plants or parasites. 
• Bladderwort and Venus fly trap are insectivorous plants and 
• Cuscuta is a parasite. 

2.5 KINGDOM ANIMALIA 

• This kingdom is characterised by heterotrophic eukaryotic organisms that are multicellular and their cells lack cell walls. 
• They directly or indirectly depend on plants for food. 
• They digest their food in an internal cavity and store food reserves as glycogen or fat. 
• Their mode of nutrition is holozoic – by ingestion of food. 
• The sexual reproduction is by copulation of male and female followed by embryological development. 

2.6 VIRUSES, VIROIDS, PRIONS AND LICHENS 

• In the five kingdom there is no mention of lichens and some acellular organisms like viruses, viroids and prions.

I. VIRUSES

• Viruses did not find a place in classification since they are not considered truly ‘living’,
• Living as those organisms that have a cell structure. 
• The viruses are non-cellular organisms that are characterised 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
• Virus means venom or poisonous fluid. 
• Viruses are obligate parasites.

Discovery of Viruses

• Dmitri Ivanowsky (1892) 

• Recognised certain microbes as causal organism of the mosaic disease of tobacco 
• These are smaller than bacteria because they passed through bacteria-proof filters. 

• M.W. Beijerinek (1898) 

• Demonstrated that the extract of the infected plants of tobacco could cause infection in healthy plants and named the new pathogen “virus” 
• They called the fluid as Contagium vivum fluidum (infectious living fluid). 

• W.M. Stanley (1935) 

• Showed that viruses could be crystallised and crystals consist largely of proteins. 
• They are inert outside their specific host cell. 

Structure of viruses

• In addition to proteins, viruses also contain genetic material (either RNA or DNA). 
• No virus contains both RNA and DNA. 
• A virus is a nucleoprotein and the genetic material is infectious. 

• Viruses that infect plants - Have single stranded RNA
• Viruses that infect animals - Have either ssRNA or dsRNA or dsDNA. 
• Viruses that infect the bacteria (bacteriophages) - Have usually dsDNA.

• Protein coat 

• Called capsid made of small subunits called capsomeres
• Protects the nucleic acid. 
• Capsomeres are arranged in helical or polyhedral geometric forms. 

Diseases causes by viruses

• In animals - mumps, small pox, herpes and influenza, AIDS
• In plants (symptoms)  - mosaic formation, leaf rolling and curling, yellowing and vein clearing, dwarfing and stunted growth.

II. Viroids

• Discovered by  T.O. Diener (In 1971)
• Smaller than viruses and caused potato spindle tuber disease. 
• It was found to be a free RNA; it lacked the protein coat, hence the name viroid. 
• The RNA of the viroid was of low molecular weight. 

III. Prions 

• They are abnormally folded protein. 
• They are similar in size to viruses. 
• Cause infectious neurological diseases
• Bovine spongiform encephalopathy (BSE) in cattle
• Cr–Jacob disease (CJD) in humans. 

• BSE commonly called mad cow disease and its analogous variant are CJD.

IV. Lichens 

• Lichens are symbiotic associations between algae and fungi. 
• Algal component (autotrophic) - known as phycobiont
• Fungal component (heterotrophic) - known as mycobiont

• Function of algae and fungi

• Algae - prepare food for fungi 
• Fungi - provide shelter and absorb mineral nutrients and water. 

• So close is their association that if one saw a lichen in nature one would never imagine that they had two different organisms within them. 
• Lichens are very good pollution indicators – they do not grow in polluted areas.