Uses of taxonomy are as follows:

• To assign each organism an appropriate place in a systematic framework of classification.
• To group animals and plants by their characteristics and relationships.
• To classify organisms based upon their similarities and differences.
• It is used for nomenclature of an organism. Assigning a name to an organism is essential for its identification without confusion throughout the scientific world.
• It is used to serve as an instrument for identification of an organisms. A newly isolated organism can be placed to its nearest relative or can be identified as a new organism with unknown characteristics.

There are three types of classification systems :

Artificial system:

• It is based on few visible, easily observable characters, which are non-evolutionary such as habit colour, form, etc.
• It does not consider the affinities (relationships) among different organisms.
• E.g. Linnaeus system of classification.

Natural system:

• It is based on objectively significant characters with respect to their affinities with other organisms.
• E.g. Bentham and Hooker's system of classification.

Phylogenetic system:

• It is based on the phylogenetic relationship between different organisms with respect to common evolutionary descent (ancestor). -
• E.g. Engler and Prantl’s classification.

Chemotaxonomy : It is a method of biological classification based on the similarities and differences in structure of certain chemical compounds present among the organisms being classified.

• It is a classification based on chemical constituents of organisms.
• For e.g. Cell wall with peptidoglycan is present in Bacteria while it is absent in Archaea.
• Among Eukarya, fungi have chitinous cell wall, while plants have cellulosic cell wall.

Numerical taxonomy: It is based on quantification of characters and develops an algorithm for classification. After comparison the organisms are grouped according to overall similarities or dissimilarity.

• The aim of this was to create a taxonomy using numeric algorithms like cluster analysis rather than using subjective evaluation of their properties
• It was proposed by Sokel and Sneath in 1963.

Applications of DNA barcoding :

The applications of DNA barcoding are as follows:

• It helps to protect endangered species.
• It plays an important role in preservation of natural resources.
• It is also used for pest control in agriculture. '
• It is used for identification of disease vectors.
• It is used for authentication of natural health products.
• It is also used for identification of medicinal plants.

Recent approaches in taxonomy :

Morphological Approach: It deals with the identification of an organism on the basis of its morphological features which are observed by naked eye or with the help of microscope.

Embryological Approach: Embryonic stages an organism helps greatly in identification. It is used in those cases whose morphological approach in less reliable.

Ecological Approach: It is based on the various habits of an organism.

Behavioral Approach / Ethological Approach: It is extremely useful in identification of closely related species. Organisms are identified on the basis of their ethological characters. These characters are genetically determined. e.g. Sound production, bioluminescence, etc.

Genetical Approach / Cytological Approach: Identification of organisms at a cellular level. It includes structural, genetical and biochemical aspects. In this DNA hybridization and karyological studies are used.

Biochemical Approach: Organisms are identified on the basis of biochemical composition. In this, Chromatography, electrophoresis and immunology techniques are used.

Numerical Taxonomy: In this method the data is numerically evaluated in the computer and similarities / differences between organisms is obtained with relative ease. After comparison the organisms are grouped according to overall similarities or dissimilarity.

Flow Chart of Taxonomic hierarchy :

Units of Classification :

Species :

• Species is the principal natural taxonomic unit, ranking below a genus, denoted by Latin binomial (considered as the basic) unit of classification.

• It is a group of organisms that can interbreed under natural condition to produce fertile offspring.
• It was thought to be an indivisible, stable and static unit.
• However, in the modem taxonomy, subdivision of species such as sub-species, varieties and populations are seen and given more importance.

Genus :

• Genus is a taxonomic rank or category larger than species used in the biological classification of living and fossil organisms.
• Genus is a group of species bearing close resemblance to one another in their morphological characters but they do not interbreed.
• For e.g. Tiger, Leopard, Lion all three belong to same genus Panthera. They have common characters yet are different from each other because their genus is same but species is different.
• Another example is genus Solanum. Brinjal and potato both belong to this genus.

Family :

• It is one of the major hierarchial taxonomic rank.
• A family represents a group of closely related genera.
• Example genera like Hibiscus, Gossypium, Sida, Bombax are included in same family Malvaceae.
• Although, there are many similarities between cat and dog, cat belongs to the family of leopards, tigers and lions, i.e. family Felidae and dog belongs to different family i.e. Canidae.

Cohort/Order :

• It is taxonomic rank used in the classification of organisms and recognised by nomenclature codes.
• An order is a group of closely related families showing definite affinities.
• Members belonging to same order but different families may show very few dissimilarities.
• Example family Papaveraceae, Brassicaceae, Capparidaceae, etc. with parietal placentation are grouped in order Parietales.
• Families of dogs and cats though are different, they belong to same order Camivora

Class :

• The class is the distinct taxonomic rank of biological classification having its own distinctive name.
• Class is the assemblage of closely allied orders.
• Example Orders Carnivora and order Primates belong to class Mammalia. Thus monkeys, gorillas, gibbons (Primates) and dogs, cats, tigers (Carnivora) belong to same class.

Division/ Phylum:

• The division is a category composed of related classes.
• Example division Angiospermae includes two classes Dicotyledonae and Monocotyledonae.
• In animal classification, instead of division, the category Phylum is used.

Sub-kingdom :

• Different divisions having some similarities form sub-kingdom.
• The divisions Angiospermae and Gymnospennae forms the sub-kingdom Phanerogams or Spermatophyta (all seed producing plants).

Kingdom :

• It is the highest taxonomic category composed of different sub-kingdoms. i
• Example sub-kingdom Phanerogams and Cryptogams form the Plant kingdom or Plantae which includes all the plants, while all animals are included in kingdom Animalia.

Classification of China-rose and Cobra :

Organisms with their Taxonomic Categories :

Disadvantages of vernacular names/ local names/ common names:

• Vemacular names do not indicate the necessary information about the organism.
• It does not indicate proper relationship of the organisms.
• Vernacular names are not universal. e.g. Pansy (Viola tricolor L.) grown in most European and American gardens has about 50 common english names.
• In Ayurveda, mango (Mangifera indica L.) is known by over 50 different names which are in Sanskrit language.
• A Vernacular names have limited usage.
• Local names are different and confusing.

Rules of binomial nomenclature:

• The name of the organism is composed of two Latin or Greek words.‘
• Generic name is a simple noun which should come first and always begin with a capital letter.
• Specific name is the descriptive adjective which should come later and begin with a small letter.
• The generic and specific name must be underlined separately if hand written or in italics when printed.
• The generic as well as specific name should not have less than three letters and more than thirteen letters.
• Usually the name of the author who names a plant or animal is also written in full or abbreviated form after scientific name. e.g. Mangifera indica L. Where L stands for Linnaeus.

Importance of Binomial nomenclature :

• The binomials are simple, meaningful and precise. .
• They are standard since they do not change from place to place.
• These names avoid confusion and uncertainty created by local or vernacular names
• The organisms are known by the same name throughout the world.
• The binomials are easy to understand and remember due to the rhyming.
• It indicates phylogeny (evolutionary history) of organisms.
• It helps to understand inter-relationship between organisms.

The criteria used by Whittaker for his system were:

• Cell organization: The organism is either prokaryotic or eukaryotic.
• Body organization: The organism is either unicellular or multicellular.
• Mode of nutrition: The organism is either autotrophic or heterotrophic
• Life style: The organism may be a producer, consumer or decomposer.

Examples:

Archaebacteria: e.g. Methanobacillus, Thiobacillus, etc.

Eubacteria: e. g. Chlorobium, Chromatium,

Cyanobacteria e.g. Nostoc, Azotobacter, etc.

On the basis of evolution, bacteria can be classified as Archaebacteria and Eubacteria.

Archaebacteria:

• These are the most primitive type of bacteria.
• They are differentiated from other bacteria on the basis of their different cellular features.
• These bacteria are mostly found in the extreme environmental conditions, hence called extremophiles. They have capacity to survive in very severe conditions. They are found in a variety of places from volcanic craters to salty lakes and hot springs.
• Bacteria that can withstand high salinities are called halophiles, while those that withstand extreme temperature are known as thermophiles.
• Methanogenic bacteria found in gut of ruminants (cows and buffaloes) help in production of methane in biogas plants.

Eubacteria:

• These are commonly referred as true bacteria.
• They have cell wall made up of peptidoglycan.
• Eubacteria are mostly heterotrophic, few are autotrophic.
• The autotrophs can be photosynthetic like Chlorobium (Green sulphur bacteria) and Chromatium or chemosynthetic like sulphur bacteria.
• These are mostly multicellular filamentous forms living in fresh water.
• Filaments show heterocyst which helps in nitrogen fixation.
• The body is covered by mucilaginous sheath.
• The genetic material is typical prokaiyotic.
• The photosynthetic pigments include Chl-a, Chl-b, carotenes and xanthophylls.
• Most of them are decomposers that help in breaking down large molecules in simple molecules or minerals.

Useful bacteria:

Most of the bacteria act as a decomposer. They breakdown large molecules in simple molecules or minerals.

Examples of some useful bacteria:

• Some bacteria helps in curdling of milk. Example- Lactobacillus.
• Helps to fix nitrogen for plants. Example- Azotobacter.
• Some bacteria like Streptomyces is used in antibiotic production such as streptomycin.
• Methanogens: These are used for production of methane (biogas) gas from dung.
• Pseudomonas spp. and Alcanovorax borkumensis: These bacteria have the ability to destroy the pyridines and other chemicals. Hence, used to clear the oil spills.

Harmful bacteria:

This includes disease causing bacteria. They cause various diseases like typhoid, cholera, tuberculosis, tetanus, etc.

Examples of some harmful bacteria:

• Salmonella typhi: It is a causative organism of typhoid.
• Vibrio cholera : It causes cholera.
• Mycobacterium tuberculosis: It causes tuberculosis.
• Clostridium tetani: It causes tetanus.
• Clostridium spp.: It causes food poisoning.
• Many forms of mycoplasma are pathogenic.

Mycoplasma : These are the smallest living cells known.

• They do not have cell wall
• Many forms are pathogenic.
• They are resistant to common antibiotics because they lack cell wall.
• Mycoplasma can survive without oxygen.

Different types of Protists :

Protists are of different types:

Plant like protista (Photosynthetic protists):

• They are termed as phytoplanktons, also known as Chrysophytes.
• They are autotrophic (photosynthetic) in nature and form major producers of ocean ecosystem.
• Most of them are referred as Diatoms because they have body wall made up of two soap-box like fitting silica covers. e.g. Diatoms.

 Animal like protists (Consumer protists):

• They are the primitive animal forms.
• They are also termed as protozoans.
• These are heterotrophic and lack cell wall.
• Amoeboid protozoans have pseudopodia as locomotory organs. E.g. Amoeba, Entamoeba.
• Amoeba is free living form, but Entamoeba is endoparasite and causes amoebic dysentery.
• Flagellated protozoans have flagella as locomotory organ. E.g. Trypanosoma.
• Cilliate protozoans have cilia for locomotion. E.g. Paramoecium.
• Plasmodium is a Sporozoan protozoa. It causes malaria. It forms spores in one of its life stages.

Dinoflagellates:

• They are aquatic (mostly marine) and autotrophic (photosynthetic).
• They have wide range of photosynthetic pigments which can be yellow, green, brown, blue and red.
• The cell wall is made up of cellulosic stiff plates.
• A pair of flagella is present, hence they are motile.
• They are responsible for famous ‘red tide’. E.g. Gonyaulax. It makes sea appear red.

Fungi like protists (Consumer decomposer protists):

• They form a group called Myxomycetes.
• They are saprophytic in nature, found on decaying leaves.
• Their cells aggregate to form a large cell mass called plasmodium.
• The spores of plasmodium are very tough and survive extreme conditions. e.g. Slime molds.

Euglenoids:

• They lack cell wall but have a tough covering of proteinaceous pellicle.
• Pellicle covering provides flexibility and contractibility to Euglena.
• They possess two flagella, one short and other long.
• They behave as heterotrophs in absence of light but possess pigments, similar to that of higher plants, for photosynthesis.

Fungi are further classified into four types on the basis of their structure, mode of spore formation and fruiting bodies as follows:

Phycomycetes:

• Members of this class are commonly called as algal fungi.
• These are consisting of aseptate coenocytic hyphae.
• They grow well in moist and damp places on decaying organic matter as well as in aquatic habitats or as parasites on plants.
• e.g. Mucor, Rhizopus (bread mold), Albugo (parasitic fungus on mustard).

Ascomycetes:

• These are commonly called as sac fungi.
• These are multicellular. They are rarely unicellular (e.g.Yeast).
• Hyphae are branched and septate.
• They can be decomposers, parasites or coprophilous (grow on dung).
• Some varieties of this class are consumed as delicacies such as morels and truffles.
• Neurospora is useful in genetic and biochemical assays.
• e.g. Aspergillus, Penicillium, Neurospora, Claviceps, Saccharomyces (unicellular ascomycetes)

Basidiomycetes :

• These are commonly called as club fungi.
• They have branched septate hyphae.
• e. g. Agaricus (mushrooms), Gernoderma (bracket fungi), Ustilago (smuts), Puccinia (rusts), etc.

Deuteromycetes:

• It is a group of fungi which are known to reproduce only asexually
• They are commonly called imperfect fungi.
• They are mainly decomposers, while few are parasitic. e. g. Alternaria.
• Deuteromycetes reproduce only by asexual spores known as conidia. When sexual stage gets discovered in species, they would be reclassified according to sexual stage.

Reproduction in fungi :

Economic importance of fungi in various sectors :

Role of fungi in medicine:

• Antibiotic penicillin is obtained from Penicillium.
• Drugs like cyclosporine, immunosuppressant drugs, precursors of steroid hormones, etc. are isolated from fungi.

Role of fungi in industries:

• Yeast is used in bread making. It causes dough to rise and make the bread light and spongy. It is also used in breweries or wine making industries. Sugars present in grapes are fermented by using yeast. This results in production of alcohol which is used for making wine.
• Lichen is a symbiotic association of algae and fungi are used in preparation of litmus paper which is used as acid-base indicator.

Role of fungi in food:

• Fungi like mushrooms are consumed as a food. These are rich source of protein.
• Fungi genus Penicillium helps in ripening of cheese.

Role of fungi as biocontrol agents:

• Fungi helps to control growth of weeds. -
• Pathogenic fungi like Fusarium sp., Phytophthora palmivora, Alternaria crassa, etc. act as mycoherbicides.

Diseases in plants :

There are different pathogens like fungi, bacteria, viruses that cause diseases in plants.

The common plant diseases are:

• Leaf rust disease: It is caused by fungus Puccinia triticina. It is the most common rust disease of wheat.
• Blight disease in rice: It is caused by harmful bacteria Xanthomonas oryzae. It causes wilting of seedlings and yellowing and drying of leaves
• Early blight of potato: It is caused by fungi Alternaria solani. It causes ‘bulls eye’ patterned leaf spots and tuber blight on potato.
• Crown gall disease: It is caused by Agrobacterium tumefaciens. This pathogen infects the plant and forms rough surfaced galls on stem and roots.

Differentiate between Plantae and Animalia :

Characteristics of Viruses :

• Viruses are acellular, highly infectious and ultramicroscopic,
• Viruses possess their own genetic material in the form of either DNA or RNA, but never both. The genetic material in viruses is covered by a protein coat (capsid), hence called nucleoprotein.
• They, do not show any activity outside the body of host; but once they enter their specific host cell, they start multiplying within the living host cells.
• Viruses lack their own metabolic machinery, they make use of the cellular machinery of the host i.e. ribosome for the synthesis of protein during their reproduction; and therefore, they cause severe infection.
• Thus, they are called infectious nucleoproteins.

Structure of virus:

• Viruses are acellular and ultramicroscopic.
• The genetic material in viruses is either single or double stranded RNA or double stranded DNA.
• Their genetic material is protected by a protein coat called capsid.
• Capsid is made up of smaller units called capsomeres.
• Capsomeres are arranged in polyhedral or helical forms thus, imparting that particular shape to the virus.

Types of viruses :

Depending upon the host, viruses are classified into three types as:

• Plant virus
• Animal virus
• Bacterial virus (Bacteriophage)

Plant virus:

• Generally, they are rod shaped or cylindrical with helical symmetry.
• Majority of plant viruses have RNA as their genetic material. (Exception: Cauliflower Mosaic Virus has double stranded DNA as genetic material)
• Plant viruses cause disease in plants. e.g. Tobacco Mosaic Virus (TMV).

Animal virus:

• Generally, they are polyhedral in shape with radial symmetry.
• They have either DNA or RNA as genetic material.
• It causes disease to majority of animals including human beings. e. g. Influenza virus.

Bacteriophage:

• They have tadpole-like shape.
• They infect bacteria and hence are called as bacteriophage.
• C. Bacteriophages were discovered by Twort.
• Bacteriophages have double stranded DNA as the genetic material.
• Its body consists of head, collar and tail.

Differentiate between viruses and viroids :

Lichens :

• Lichen is co-existence of algae and fungi for mutual benefit.
• It is the best example of symbiosis or mutualism.
• They are found in extreme environments like snow clad poles.
• The algal component of lichen is phycobiont mostly belong to cyanobacteria (blue-green algae) or green algae and fungal component is mycobiont.
• Algae prepares the food and supplies it to the fungal component, while fungal component provides shelter to algae and also absorbs water and minerals for algae.
• The association is intense and it is difficult to identify them as separate living beings.
• They are very sensitive to pollutions, hence not found in polluted areas.
• They are used as pollution indicators.
• They play an important role in soil formation by using specific acid productions.