BIOLOGICAL CLASSIFICATION

Introduction

• In Linnaeus time a Two Kingdom system of classification with Plantae and Animalia kingdoms was developed that included all plants and animals respectively.
• This system did not distinguish between the eukaryotes and prokaryotes, unicellular and multicellular organisms and photosynthetic (green algae) and non-photosynthetic (fungi) organisms.
• Classification of organisms into plants and animals was easily done and was easy to understand, but, a large number of organisms did not fall into either category.
• Two kingdom classification used for a long time was found inadequate.
• Classification systems for the living organisms have hence, undergone several changes over the time.
• Though plant and animal kingdoms have been a constant under all different systems.
• The understanding of what groups/organisms be included under these kingdoms have been changing; the number and nature of other kingdoms have also been understood differently by different scientists over the time.
• R.H. Whittaker (1969) proposed a Five Kingdom Classification. 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.
• The three-domain system has also been proposed that divides the Kingdom Monera into two domains, leaving the remaining eukaryotic kingdoms in the third domain and thereby a six kingdom classification.
• 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.
• This placed together groups which widely differed in other characteristics.

Characteristics of Five Kingdoms

• It brought together the prokaryotic bacteria and the blue green algae (cyanobacteria) with other groups which were eukaryotic.
• It also grouped together the unicellular organisms and the multicellular ones, say, for example, Chlamydomonas and Spirogyra were placed together under algae.
• The classification did not differentiate between the heterotrophic group - fungi, and the autotrophic green plants, though they also showed a characteristic difference in their walls composition - the fungi had chitin in their walls while the green plants had a cellulosic cell wall.
• Fungi were placed in a separate kingdom - Kingdom Fungi. All prokaryotic organisms were grouped together under Kingdom Monera and the unicellular eukaryotic organisms were placed in Kingdom Protista.
• Protista has brought together Chlamydomonas, ChIarella (earlier placed in Algae within Plants and both having cell walls) with Paramoecium and Amoeba. It has put together organisms which, in earlier classifications, were placed in different kingdoms.
• This happened because the criteria for classification changed. This kind of changes will take place in future too depending on the improvement in our understanding of characteristics and evolutionary relationships.

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: the spherical Coccus (pI.: cocci), the rod-shaped Bacillus (pI.: bacilli), the comma-shaped Vibrium (pI.: vibrio) and the spiral Spirillum (pI.: spirilla).

• 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. 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.

Archaebacteria

• These bacteria are special since they live in some of the most harsh habitats such as extreme salty areas (halophiles), hot springs (thermoacidophiles) and 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 of these animals.

Eubacteria

• There are thousands of different eubacteria or ‘true bacteria’.
• They are characterized by the presence of a rigid cell wall, and if motile, a flagellum. 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.
• Chemosynthetic autotrophic 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.
• 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. Bacteria reproduce mainly by fission.

• Sometimes, under unfavourable 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.
• 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.

Kingdom Protista

• All single-celled eukaryotes are placed under Protista, but the boundaries of this kingdom are not well defined. Chrysophytes, Dinoflagellates, Euglenoids, Slime moulds and Protozoans under Protista.
• Members of Protista are primarily aquatic.
• This kingdom forms a link with the others dealing with plants, animals and fungi.
• Being eukaryotes, the protistan cell body contains a well defined nucleus and other membrane-bound organelles.
• Some have flagella or cilia. Protists reproduce asexually and sexually by a process involving cell fusion and zygote formation.

Chrysophytes

• This group includes diatoms and golden algae (desmids). They are found in fresh water as well as in 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 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 ocean.

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.
• 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.

Euglenoids

• Majority of them are fresh water organisms found in stagnant water.
• 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.
• Though they are photosynthetic in the presence of sunlight, when deprived of sunlight they behave like heterotrophs by predating on other smaller organisms. The pigments of euglenoids are identical to those present in higher plants. Example: Euglena (Figure 2.4).

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 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.

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.
• 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.
• 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. 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.
• 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.

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. White spots seen on mustard leaves are due to a parasitic fungus.
• Some unicellular fungi, e.g., yeast are used to make bread and beer.
• Other fungi cause diseases in plants and animals; wheat rust-causing Puccinia is an important example.
• Some are the source of antibiotics, e.g., Penicillium.
• Fungi are cosmopolitan and occur in air, water, soil and on animals and plants. They prefer to grow in warm and humid places.
• 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.
• Some hyphae are continuous tubes filled with multinucleated cytoplasm - these are called coenocytic hyphae.
• Others have septae or cross walls in their hyphae.
• The cell walls of fungi are composed of chitin and polysaccharides.
• Most fungi are heterotrophic and absorb soluble organic matter from dead substrates and hence are 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 can take place by vegetative means- fragmentation, fission and budding. Asexual reproduction is by spores called conidia or sporangiospores or zoospores, and sexual reproduction is by oospores, ascospores and basidiospores.
• The various spores are produced in distinct structures called fruiting bodies.
• The sexual cycle involves the following three steps: Fusion of protoplasms between two motile or non-motile gametes called plasmogamy. Fusion of two nuclei called karyogamy. 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).
• 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.
• 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.

Phycomycetes

• Members of phycomycetes are found in aquatic habitats and on decaying wood in moist and damp places or as obligate parasites on plants.
• The mycelium is aseptate and coenocytic.
• Asexual reproduction takes place by zoospores (motile) or by aplanospores (non-motile).
• These spores are endogenously produced in sporangium.
• 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).

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).
• Mycelium is branched and septate.
• The asexual spores are conidia produced exogenously on the special mycelium called conidiophores.
• Conidia on germination produce mycelium.
• 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.
• Some examples are Aspergillus, Claviceps and Neurospora.
• Neurospora is used extensively in biochemical and genetic work.
• Many members like morels and truffles are edible and are considered delicacies.

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.
• The mycelium is branched and septate.
• The asexual spores are generally not found, but vegetative reproduction by fragmentation is common.
• 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 (pI.: basidia).
• The basidia are arranged in fruiting bodies called basidiocarps.
• Some common members are Agaricus (mushroom) (Figure 2.5c), Ustilago (smut) and Puccinia (rust fungus).

Deuteromycetes

• Commonly known as imperfect fungi because only the asexual or vegetative phases of these fungi are known.
• When the sexual forms of these fungi were discovered they were moved into classes they rightly belong to.
• It is also possible that the asexual and vegetative stage have been given one name (and placed under deuteromycetes) and the sexual stage another (and placed under another class).
• Once perfect (sexual) stages of members of dueteromycetes were discovered they were often moved to ascomycetes and basidiomycetes.
• The deuteromycetes reproduce only by asexual spores known as conidia.
• The mycelium is septate and branched.
• Some members are saprophytes or parasites while a large number of them are decomposers of litter and help in mineral cycling.
• Some examples are Alternaria, Colletotrichum and Trichoderma.

Kingdom Plantae

• Kingdom Plantae includes all eukaryotic chlorophyll- containing organisms commonly called plants.
• Bladderwort and Venus fly trap are examples of insectivorous plants and Cuscuta is a parasite. The plant cells have an eukaryotic structure with prominent chloroplasts and cell wall mainly made of cellulose.
• Plantae includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms.
• Life cycle of plants has two distinct phases - the diploid sporophytic and the haploid gametophytic - that alternate with each other.
• The lengths of the haploid and diploid phases, and whether these phases are free- living or dependent on others, vary among different groups in plants. This phenomenon is called alternation of generation.

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.
• They follow a definite growth pattern and grow into adults that have a definite shape and size.
• Higher forms show elaborate sensory and neuromotor mechanism. Most of them are capable of locomotion.
• The sexual reproduction is by copulation of male and female followed by embryological development.

Viruses, Viroids, Prions and Lichens

• In the five kingdom classification of Whittaker there is no mention of lichens and some acellular organisms like viruses, viroids and prions.
• All of us who have suffered the ill effects of common cold or ‘flu’ know what effects viruses can have on us, even if we do not associate it with our condition.
• Viruses did not find a place in classification since they are not considered truly ‘living’.
• The viruses are non-cellular organisms that are characterised by having an inert crystalline structure outside the living cell.
• The name virus that means venom or poisonous fluid was given by Dmitri Ivanowsky (1892) recognised certain microbes as causal organism of the mosaic disease of tobacco.            
• These were found to be 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” and 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. Viruses are obligate parasites.
• 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 (viruses that infect the bacteria) are usually double stranded DNA viruses.
• The protein coat called capsid made of small subunits called capsomeres, protects the nucleic acid.
• These capsomeres are arranged in helical or polyhedral geometric forms. Viruses cause diseases like mumps, small pox, herpes and influenza.
• AIDS in humans is also caused by a virus. In plants, the symptoms can be mosaic formation, leaf rolling and curling, yellowing and vein clearing, dwarfing and stunted growth.
• 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, locked protein coat that is found in virus, hence the name viroid.
• The RNA of the viroid was of low molecular weight.
• 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 Cr-Jacob disease (CJD) in humans.
• Lichens are symbiotic associations i.e. mutually useful associations, between algae and fungi.
• The algal component is known as phycobiont and fungal component as mycobiont, which are autotrophic and 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 - they do not grow in polluted areas.

NEET SPECIAL

• Cladistics - approach to biological classification in which organisms are categorized in groups (“clades”) based on the most recent common ancestor.
• Cladogram - outcome of a cladistic analysis, a tree-shaped diagram (dendrogram) interpreted to represent the best hypothesis of phylogenetic relationships.
• Anhaima - animals without blood.
• Enhaima - animals with blood.
• Andrea Cesalpino (1519-1603) - called “the first taxonomist”, wrote De Plantis in 1583.
• Carl Woese - proposed in 1977 a three, domain system, separation of Archaea and Bacteria.
• Heckel - in 1866 gave three kingdom system: Plantae, Protista and Animalia.
• Copelnad - in 1938 gave four kingdom system: Monera, Protista, Plantae and Animalia.
• Cavalier-Smith - gave six & seven kingdom system in 1998 & 2015 respectively.
• Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source and other species of archaea fix carbon.
• One of the most extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0.
• The methanogen Methanobrevibacter smithii is the most common archaean in the human flora, making up about 10% of all the prokaryotes in the human gut.
• Most bacteria have the Gram-negative cell wall, and only the Firmicutes and Actinobacteria have the alternative Gram-positive arrangement.
• Antibiotics like vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.
• Mycoplasmal bacteria are also known as Mollicutes.
• Protophyta: These “plant-like” (autotrophic) organisms are composed mostly of unicellular algae. The dinoflagellates, diatoms and Euglena-like flagellates are photosynthetic protists.
• Ambiregnal protists: Some protists considered being both protozoa and algae or fungi e.g., slime molds and flagellated algae.
• Amphiesma : A complex cell covering composed of a series of membranes, flattened vesicles called alveola in Dinoflagellates.
• The dinoflagellate Erythropsidium has the smallest known eye.
• ‘Core dinoflagellates’ (dinokaryotes) have a peculiar form of nucleus, called a dinokaryon, in which the chromosomes are attached to the nuclear membrane.
• The Myxogastria, are the only macroscopic slime molds.