Chapter 2 — Biological Classification

Biological classification is the scientific procedure of arranging organisms into groups and subgroups on the basis of their similarities and differences. The earliest systematic attempt was made by Aristotle, who used simple morphological characters to classify plants into trees, shrubs and herbs, and animals into those with red blood and those without. Such systems grouped by convenience rather than by relationship.

Linnaeus in the eighteenth century proposed the two-kingdom system: kingdom Plantae for plants and kingdom Animalia for animals. This served for two centuries and is still the everyday view. But as microscopes improved and more organisms were studied, the two-kingdom system showed serious weaknesses. It did not distinguish between prokaryotes, whose cells lack a true nucleus, and eukaryotes, whose cells have one; between unicellular and multicellular organisms; or between photosynthetic organisms such as green algae and non-photosynthetic organisms such as fungi, which were both lumped with plants. Euglena, which has chlorophyll but also moves and ingests food, fell into both kingdoms at once. Bacteria, which resemble neither plants nor animals, were forced into Plantae because they have a cell wall. Fungi, which have chitin walls and absorb food, were called plants although they have nothing plant-like except immobility.

Various intermediate proposals followed: Haeckel's three kingdoms (Protista for unicellular organisms), Copeland's four (adding Monera for prokaryotes). Then in 1969 R. H. Whittaker proposed the five-kingdom classification: Monera, Protista, Fungi, Plantae and Animalia. The main criteria he used were:

• Cell structure: prokaryotic (Monera) or eukaryotic (the other four).
• Body organisation: unicellular (Monera, Protista) or multicellular (Fungi, Plantae, Animalia), with the fungal body as a loose tissue of hyphae.
• Mode of nutrition: autotrophic (photosynthetic or chemosynthetic) or heterotrophic; and among heterotrophs, absorptive (Fungi) or ingestive (Animalia).
• Reproduction and phylogenetic relationships.

The five-kingdom system placed all prokaryotes in Monera, all unicellular eukaryotes in Protista, the fungi in a kingdom of their own, and left Plantae for the multicellular photosynthetic eukaryotes and Animalia for the multicellular ingestive ones. It thus separated organisms by fundamental cell type and by the three great modes of nutrition, production, absorption and ingestion, and it reflected evolutionary history: prokaryotes first, then unicellular eukaryotes, then three multicellular lines diverging from protistan ancestors.

The system has its own problems. Protista is a grab-bag of unrelated lineages; the chlorophyll-bearing algae are split between Protista and Plantae; and viruses, which are not cellular, have no place at all. In recent decades Carl Woese proposed three domains, Bacteria, Archaea and Eukarya, above the kingdoms, on the basis of ribosomal RNA sequences, and a six-kingdom system splitting Monera into Archaebacteria and Eubacteria is now widely taught. For this course, however, the five-kingdom system is the framework, and the remaining topics describe each kingdom in turn.

Kingdom Monera includes all prokaryotes, and bacteria are its sole members. They are the most abundant micro-organisms on earth. Bacteria occur almost everywhere: hundreds of them are present in a handful of soil; they live in extreme habitats such as hot springs, deserts, snow and deep oceans where few other life forms survive; and many live in or on other organisms as parasites or symbionts.

Cell structure. A bacterial cell has a cell wall made of peptidoglycan (murein), not cellulose, outside a plasma membrane. There is no nuclear membrane; the single circular DNA molecule lies naked in the cytoplasm as a nucleoid. There are no membrane-bound organelles: no mitochondria, chloroplasts, endoplasmic reticulum or Golgi bodies. Ribosomes are of the smaller 70S type. Many bacteria carry small extra rings of DNA called plasmids, may be surrounded by a slimy capsule, and may bear flagella for movement and pili for attachment. Some form resistant endospores that survive heat and drought.

Shapes. Bacteria are grouped into four categories on the basis of shape: the spherical coccus (plural cocci), the rod-shaped bacillus (bacilli), the comma-shaped vibrio (vibrios) and the spiral spirillum (spirilla). Cocci may occur in pairs (diplococci), chains (streptococci) or clusters (staphylococci).

Nutrition. Though the structure of bacteria is very simple, they are very complex in behaviour. Compared with many other organisms bacteria as a group show the most extensive metabolic diversity. Some are autotrophic: they synthesise their own food from inorganic substrates, either using light (photosynthetic autotrophs, such as cyanobacteria and the purple and green sulphur bacteria) or using the energy of chemical oxidation (chemosynthetic autotrophs, such as nitrifying, sulphur and iron bacteria). The majority are heterotrophic: they depend on other organisms or on dead organic matter for food, as saprophytes, parasites or symbionts.

Reproduction. Bacteria reproduce mainly by binary fission: the cell elongates, the DNA replicates, and the cell divides into two equal daughter cells, in as little as twenty minutes under favourable conditions. Under unfavourable conditions they produce spores. They also reproduce by a sort of sexual reproduction in which DNA passes from one bacterium to another through conjugation (via a pilus), transformation (uptake of free DNA from the surroundings) or transduction (transfer by a bacteriophage); there is no fusion of gametes, only one-way transfer of genetic material.

Importance. Heterotrophic bacteria are the most abundant in nature and the majority are important decomposers, returning nutrients to the soil. Many are helpful in making curd from milk, producing antibiotics, fixing nitrogen in legume roots and treating sewage. Others are pathogens causing damage to human beings, crops, farm animals and pets: cholera, typhoid, tetanus, tuberculosis and citrus canker are all bacterial diseases.

Monera is divided into two main groups, Archaebacteria and Eubacteria, described in the following topics, together with the special cases of cyanobacteria and mycoplasma.

Archaebacteria are a group of bacteria that live in the most harsh habitats on earth, and for that reason are often called extremophiles. They are considered the most primitive living organisms, close to the earliest forms of life, and the name archae- means ancient. They differ from other bacteria, the eubacteria, in the composition of their cell wall and membrane and in their genetic machinery, and these differences are so deep that Woese placed them in a separate domain, Archaea, closer in some respects to eukaryotes than to true bacteria.

Distinctive features. The cell wall of archaebacteria lacks peptidoglycan; it is made of proteins, glycoproteins or polysaccharides (pseudomurein in some). The membrane lipids are built on branched-chain hydrocarbons linked to glycerol by ether bonds, instead of the straight-chain fatty acids with ester bonds found in all other organisms; this unusual membrane resists heat, acid and salt. Their ribosomal RNA sequences and their RNA polymerase and histone-like proteins resemble those of eukaryotes. These features enable them to survive in extreme conditions.

Three groups are recognised by habitat:

• Halophiles (salt-loving) live in extremely salty areas such as salt pans, salt lakes and the Dead Sea, where the salt concentration may be ten times that of sea water. Halobacterium contains a purple pigment, bacteriorhodopsin, with which it captures light energy.
• Thermoacidophiles live in hot springs and volcanic vents where the water is near boiling and strongly acidic; Sulfolobus grows at 80 °C and pH 2, oxidising sulphur for energy. Some hyperthermophiles at deep-sea vents grow above 100 °C.
• Methanogens live in marshy areas and in the gut of several ruminant animals such as cows and buffaloes, where they produce methane by reducing carbon dioxide with hydrogen in the complete absence of oxygen; they are strict anaerobes. Methanobacterium is the common example. They are responsible for the production of methane (biogas) from the dung of these animals, and the gobar-gas plant is essentially a methanogen culture.

Importance. Methanogens supply biogas in rural energy schemes and are part of the treatment of sewage sludge. Thermophilic archaebacteria are the source of heat-stable enzymes used in industry and in the polymerase chain reaction of molecular biology. The study of extremophiles guides the search for life on other planets. And the discovery that these organisms are genetically as distant from eubacteria as both are from eukaryotes reshaped the tree of life into three domains.

In the examination, archaebacteria are asked as a short-answer question: name the three groups with their habitats, and state the wall and membrane differences that let them survive. A frequently asked one-liner is 'Which bacteria are found in the gut of ruminants and what do they produce?', with the answer methanogens and methane.

Eubacteria, the true bacteria, are thousands in number and are characterised by the presence of a rigid cell wall of peptidoglycan and, if motile, a flagellum. They include nearly all the familiar bacteria of soil, water, food and disease, and their metabolic diversity is unmatched. Two groups deserve separate mention because of their special nutrition: the photosynthetic cyanobacteria and the chemosynthetic autotrophs; a third, the mycoplasmas, is treated in the next topic.

Cyanobacteria (also called blue-green algae) are photosynthetic autotrophs. They have chlorophyll a similar to green plants, together with the accessory pigments phycocyanin (blue) and phycoerythrin (red), and they release oxygen in photosynthesis, as plants do; it was cyanobacteria that first oxygenated the earth's atmosphere. Their pigments are not enclosed in chloroplasts but lie on membranes (thylakoids) free in the cytoplasm, as befits prokaryotes. The cyanobacteria are unicellular, colonial or filamentous, freshwater, marine or terrestrial. The colonies are generally surrounded by a gelatinous sheath. They often form blooms in polluted water bodies, colouring the surface and depleting oxygen when they decay.

Some of these organisms can fix atmospheric nitrogen in specialised cells called heterocysts: large, thick-walled, pale cells at intervals along the filament, in which the oxygen-sensitive enzyme nitrogenase is protected from the oxygen produced by the neighbouring photosynthetic cells. Nostoc and Anabaena are the classic examples. Because they both photosynthesise and fix nitrogen, these organisms are used as biofertilisers in paddy fields; Anabaena living in the leaves of the water fern Azolla is a traditional green manure of rice cultivation. Oscillatoria is a common filamentous form without heterocysts, and Spirulina is cultivated as a protein-rich food supplement.

Chemosynthetic autotrophic bacteria oxidise various inorganic substances such as nitrates, nitrites and ammonia, and use the released energy for their ATP production and for fixing carbon dioxide. They play a great role in recycling nutrients like nitrogen, phosphorus, iron and sulphur. The nitrifying bacteria Nitrosomonas (ammonia to nitrite) and Nitrobacter (nitrite to nitrate) convert the ammonia of decay into the nitrate that plants absorb; sulphur bacteria such as Thiobacillus oxidise hydrogen sulphide and sulphur to sulphate; iron bacteria oxidise ferrous to ferric iron. These bacteria do not need light and are the producers of the deep-sea vent communities and of the dark soil.

Heterotrophic eubacteria are the most abundant in nature. As saprophytic decomposers they break down dead organic matter; as symbionts they fix nitrogen in root nodules (Rhizobium) and digest cellulose in the gut of herbivores; in industry they make curd (Lactobacillus), vinegar (Acetobacter), antibiotics (Streptomyces) and many enzymes; as pathogens they cause cholera (Vibrio cholerae), typhoid (Salmonella typhi), tetanus (Clostridium tetani), tuberculosis (Mycobacterium tuberculosis) and, in plants, citrus canker (Xanthomonas citri) and crown gall (Agrobacterium tumefaciens).

The examination asks for the characters of cyanobacteria, the function of heterocysts, and examples of chemosynthetic and pathogenic bacteria; the names in this topic should be learnt with their roles.

The mycoplasmas are the odd members of kingdom Monera. They are organisms that completely lack a cell wall, and they are the smallest living cells known, about 0.1 to 0.3 micrometre in diameter, smaller than some viruses. Because they have no rigid wall, their shape is not fixed: the same species may appear as spheres, filaments, rings or branched forms, a condition called pleomorphism. Being wall-less, they can pass through bacterial filters and are naturally resistant to antibiotics such as penicillin that act on cell wall synthesis; they are, however, sensitive to tetracyclines and erythromycin, which act on protein synthesis.

The mycoplasma cell is bounded only by a plasma membrane that is unusually rich in sterols, which it takes up from its host and which give the membrane the strength a wall would otherwise provide. Inside is the smallest genome of any free-living organism, a few hundred genes on one circular DNA molecule, together with 70S ribosomes. There are no organelles. Mycoplasmas can survive without oxygen and are cultured on complex media containing serum; the colonies on agar have a characteristic fried-egg appearance.

Many mycoplasmas are pathogenic in animals and plants. Mycoplasma pneumoniae causes primary atypical pneumonia (walking pneumonia) in human beings, and other species cause urogenital infections and, in cattle, contagious pleuropneumonia; indeed the group was first isolated from cattle and was long called PPLO, pleuropneumonia-like organisms. In plants, mycoplasma-like organisms (now called phytoplasmas) live in the phloem sieve tubes and are transmitted by leaf-hoppers, causing witches' broom of legumes, little leaf of brinjal, sandal spike, sesamum phyllody and grassy shoot of sugarcane. The plant diseases are characterised by yellowing, stunting, proliferation of shoots and conversion of flower parts into leafy structures, and they were mistaken for virus diseases until the organisms were seen in the phloem in 1967.

Mycoplasmas are placed in Monera because they are prokaryotes: no nuclear membrane, no organelles, small ribosomes, a single circular chromosome and binary fission. They are thought to have evolved from walled Gram-positive bacteria by loss of the wall genes, a reduction that fits their parasitic way of life inside hosts where the osmotic environment is stable.

The examination's favourite questions on mycoplasma are one-liners: 'Name the smallest living cell', 'Which organisms lack a cell wall entirely', 'Why are mycoplasmas resistant to penicillin', and 'Name two plant diseases caused by mycoplasma'. The points to remember are: no cell wall, smallest cells, pleomorphic, anaerobic survival, penicillin-resistant, pathogenic to animals and plants, and the disease list above.

All single-celled eukaryotes are placed under kingdom Protista, but the boundaries of this kingdom are not well defined. What may be a photosynthetic protistan to one biologist may be a plant to another; the kingdom is defined more by what its members are not (not prokaryotes, not multicellular fungi, plants or animals) than by what they are. In this course kingdom Protista includes the chrysophytes, dinoflagellates, euglenoids, slime moulds and protozoans.

General characters. Members of Protista are primarily aquatic, found in fresh water, the sea and moist soil. Being eukaryotes, the protistan cell body contains a well-defined nucleus and membrane-bound organelles such as mitochondria, endoplasmic reticulum and, in the photosynthetic forms, chloroplasts. Some have flagella or cilia for movement, others move by pseudopodia or gliding, and some are non-motile. Nutrition may be photosynthetic (autotrophic), holozoic (ingesting food particles, as in Amoeba), saprobic (absorbing dissolved organic matter) or parasitic; some, such as Euglena, switch between modes. Protists reproduce asexually by binary fission or spores and sexually by a process involving cell fusion and zygote formation; the life cycles are varied. Protista forms a link with the other kingdoms of plants, animals and fungi, each of which is thought to have arisen from protistan ancestors.

Chrysophytes. This group includes the diatoms and the golden algae (desmids). They are found in fresh water as well as in marine environments, and they are microscopic and float passively in water currents, forming a large part of the plankton. Most of them are photosynthetic, with chlorophylls a and c and the golden-brown pigment fucoxanthin, and store food as oils and the polysaccharide chrysolaminarin. In diatoms the cell walls form two thin overlapping shells, which fit together as in a soap box, one half (the epitheca) overlapping the other (the hypotheca). The walls are embedded with silica and thus 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, in filtration of oils and syrups, in toothpaste and as an insulator and insecticide. Diatoms are the chief producers in the oceans, responsible for a large fraction of the earth's photosynthesis. They reproduce by cell division, each daughter cell keeping one shell and secreting a new smaller inner one, so that the average size declines until sexual reproduction restores it.

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 (chlorophylls a and c, carotenoids and peridinin). The cell wall has stiff cellulose plates on the outer surface, giving an armoured appearance. Most of them have two flagella: one lies longitudinally and the other transversely in a furrow between the wall plates, and their beating spins the cell as it moves. Very often, red dinoflagellates (for example Gonyaulax) undergo such rapid multiplication that they make the sea appear red, the phenomenon of red tides. Toxins released by such large numbers may even kill other marine animals such as fishes and can poison humans who eat contaminated shellfish. Some dinoflagellates such as Noctiluca are bioluminescent, lighting the waves at night. A few are parasitic and a few live symbiotically inside corals as zooxanthellae, supplying the reef with food.

Euglenoids. Majority of them 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, so that Euglena can change shape as it moves. They have two flagella, a short and a long one, arising from a reservoir at the anterior end; near the reservoir is a red eye spot (stigma) that helps the cell orient toward light. Though they are photosynthetic in the presence of sunlight, when deprived of sunlight they behave like heterotrophs by predating on other smaller organisms or absorbing organic matter; this dual nutrition is called mixotrophy. Interestingly, the pigments of euglenoids are identical to those present in higher plants: chlorophylls a and b. They store food as paramylon, a polysaccharide different from starch. A contractile vacuole regulates water content. Reproduction is by longitudinal binary fission; sexual reproduction is unknown. Euglena is the example. The combination of plant-like pigments and animal-like movement and feeding made euglenoids the classic problem of the two-kingdom system and a natural member of Protista.

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 a plasmodium, which may grow and spread over several feet; it is a multinucleate mass of protoplasm without cell walls, moving like a giant Amoeba. 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. Slime moulds were once placed with fungi because of their spore-bearing fruiting bodies, but their amoeboid feeding stage and lack of chitin show they are protists. Physarum is the common plasmodial slime mould; the cellular slime moulds such as Dictyostelium live as separate amoebae that aggregate only to form a fruiting body.

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:

• 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 (radiolarians) or calcareous shells (foraminifera). Some of them such as Entamoeba histolytica are parasites, causing amoebic dysentery.
• Flagellated protozoans are either free-living or parasitic. They have flagella. The parasitic forms cause diseases such as sleeping sickness, caused by Trypanosoma and spread by the tsetse fly; Giardia and Leishmania (kala-azar) are other parasites.
• Ciliated protozoans 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. Paramecium is the example, with its two nuclei, a macronucleus and a micronucleus.
• Sporozoans include diverse organisms that have an infectious spore-like stage in their life cycle. They have no locomotory organelles and are all parasites. The most notorious is Plasmodium, the malarial parasite, which causes malaria, a disease that has a staggering effect on the human population and is spread by the female Anopheles mosquito.

These five groups of Protista are the standard examination list; a common question asks for a table of their habitat, cell covering, locomotion, nutrition and an example.

The fungi constitute a unique kingdom of heterotrophic organisms. They show a great diversity in morphology and habitat. Everyone has seen fungi: the mould on moist bread and rotten fruits, the mushrooms after rain, the yeast used in bread and beer, the white spots on mustard leaves caused by a parasitic fungus. Some unicellular fungi such as yeast are used to make bread and beer; other fungi cause diseases in plants and animals, wheat rust caused by Puccinia being a classic example; some are the source of antibiotics such as penicillin from Penicillium. Fungi are cosmopolitan and occur in air, water, soil and on animals and plants. They prefer to grow in warm and humid places, which is why we keep food in the refrigerator.

Body. 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. Some hyphae are continuous tubes filled with multinucleated cytoplasm; these are called coenocytic hyphae. Others have septa or cross walls in their hyphae, and are septate. The cell walls of fungi are composed of chitin and polysaccharides, never cellulose alone; chitin is the polymer that also forms the exoskeleton of insects. Food is stored as glycogen and oil, as in animals, never as starch.

Nutrition. Most fungi are heterotrophic and absorb soluble organic matter from dead substrates and hence are called saprophytes. They secrete digestive enzymes onto the substrate and absorb the products through the hyphal wall, so digestion is external. Those that depend on living plants and animals are called parasites, obligate or facultative. They can also live as symbionts: in association with algae as lichens, and with roots of higher plants as mycorrhiza, in which the fungus supplies minerals and water to the root and receives sugars.

Reproduction in fungi can take place by vegetative means: fragmentation, fission and budding. Asexual reproduction is by spores called conidia (formed externally on conidiophores) or sporangiospores (formed inside a sporangium) or zoospores (motile, in aquatic forms). Sexual reproduction is by oospores, ascospores and basidiospores. The various spores are produced in distinct structures called fruiting bodies. 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 the 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 a diploid cell (2n). However, in other fungi (ascomycetes and basidiomycetes), an intervening dikaryotic stage (n + n, two nuclei per cell) occurs; such a condition is called a dikaryon and the phase is called dikaryophase. Later the parental nuclei fuse and the cell becomes diploid. The fungi form fruiting bodies in which reduction division occurs, leading to the formation of haploid spores.

The morphology of the mycelium, the mode of spore formation and the fruiting bodies form the basis for the division of the kingdom into four classes: Phycomycetes, Ascomycetes, Basidiomycetes and Deuteromycetes, described next.

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 name means alga-like fungi, because their coenocytic mycelium and motile spores resemble those of some algae. The mycelium is aseptate and coenocytic: a branching tube with many nuclei and no cross walls except where reproductive organs are cut off. Asexual reproduction takes place by zoospores (motile, with flagella, in aquatic forms) or by aplanospores (non-motile), and these spores are endogenously produced in a sporangium. A zygospore is formed by the 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) and Albugo (the parasitic fungus causing white rust on mustard).

Rhizopus illustrates the class. Its mycelium spreads over bread as a white cottony mass with root-like rhizoids and runner-like stolons; upright sporangiophores bear black globular sporangia whose sporangiospores blow away to start new colonies. When two compatible mycelia meet, their hyphal tips swell into gametangia that fuse to form a thick-walled black zygospore, which after rest undergoes meiosis and germinates into a sporangium. Albugo candida forms white blisters on the leaves and stems of mustard and other crucifers, its sporangia bursting through the epidermis as a white powder, and produces oospores inside the host tissue.

Ascomycetes. Commonly known as sac-fungi, the ascomycetes are mostly multicellular (for example Penicillium) or rarely unicellular (yeasts, Saccharomyces). They are saprophytic, decomposers, parasitic or coprophilous (growing on dung). The mycelium is branched and septate. The asexual spores are conidia, produced exogenously on special mycelial branches called conidiophores; conidia on germination produce mycelium. Sexual spores are called ascospores, which are produced endogenously in sac-like structures called asci (singular ascus), usually eight in each ascus, after karyogamy and meiosis followed by one mitosis. The asci are arranged in different types of fruiting bodies called ascocarps: closed (cleistothecium, as in Penicillium), flask-shaped with a pore (perithecium, as in Claviceps) or cup-shaped (apothecium, as in Peziza and the morels). Some examples are Aspergillus, Claviceps and Neurospora. Neurospora is used extensively in biochemical and genetic work, since its ordered ascospores show the results of meiosis directly. Many members like morels and truffles are edible and are considered delicacies.

Other important ascomycetes: Saccharomyces cerevisiae, the baker's and brewer's yeast, which ferments sugar to alcohol and carbon dioxide and reproduces by budding; Penicillium notatum and P. chrysogenum, the source of penicillin; Aspergillus niger, used to produce citric acid; and Claviceps purpurea, the ergot of rye, whose alkaloids are both poisons and medicines.

The examination asks for a comparison of the two classes: mycelium (coenocytic versus septate), asexual spores (endogenous sporangiospores versus exogenous conidia), sexual spores (zygospore or oospore versus ascospores in asci), and two examples each. The table in the next topic gathers all four classes.

Basidiomycetes. Commonly known as mushrooms, bracket fungi or puffballs, the basidiomycetes grow in soil, on logs and tree stumps and in living plant bodies as parasites, for example rusts and smuts. The mycelium is branched and septate, and the septa have a central pore with a swollen rim (dolipore) through which cytoplasm but not nuclei can pass. 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 (n + n), which ultimately gives rise to a basidium, a club-shaped cell. Karyogamy and meiosis take place in the basidium, producing four basidiospores, which are borne exogenously on small stalks (sterigmata) at the tip of the basidium. The basidia are arranged in fruiting bodies called basidiocarps: the familiar mushroom is a basidiocarp, with basidia lining the gills under its cap. Some common members are Agaricus (the edible mushroom), Ustilago (smut) and Puccinia (the rust fungus).

Clamp connections, small bridges between adjacent cells of the dikaryotic mycelium, are characteristic of the class and ensure that each cell receives one nucleus of each type at division. The dikaryotic phase is long, often the main phase of the life cycle; the diploid stage is confined to the basidium itself. Puccinia graminis tritici, the black stem rust of wheat, completes its life cycle on two hosts, wheat and barberry, producing five kinds of spores, and was the subject of pioneering plant pathology work in India by K. C. Mehta. Ustilago smuts replace the grain of cereals with black spore masses. Bracket fungi (Polyporus, Ganoderma) decay timber; puffballs (Lycoperdon) release clouds of spores when ripe. Edible species include the button mushroom Agaricus bisporus, the oyster mushroom Pleurotus and the paddy-straw mushroom Volvariella, all cultivated commercially in Telangana.

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 the classes they rightly belong to; it is also possible that the asexual and vegetative stage had been given one name and the sexual stage another. Later when the linkages were established, the fungi were correctly identified and moved out of Deuteromycetes. Once perfect (sexual) stages of members of Deuteromycetes were discovered they were often moved to Ascomycetes and Basidiomycetes. The class is thus an artificial holding group, a form-class, rather than a natural taxon. 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 (early blight of potato, leaf spots), Colletotrichum (anthracnose of many crops) and Trichoderma (a soil fungus used as a biocontrol agent against root pathogens). Many Aspergillus and Penicillium species were once here before their ascus stages were found. Several deuteromycetes cause skin diseases in humans (ringworm, athlete's foot).

Kingdom Plantae includes all eukaryotic chlorophyll-containing organisms commonly called plants. A few members are partially heterotrophic, such as the insectivorous plants and the parasites. Bladderwort (Utricularia) and Venus fly trap (Dionaea) are examples of insectivorous plants that supplement their nitrogen by trapping insects, and Cuscuta (dodder), a leafless yellow twiner, is a total parasite drawing food from its host through haustoria. The plant cells have a eukaryotic structure with prominent chloroplasts and a cell wall mainly made of cellulose. Food is stored as starch. Plants are non-motile as a whole, though gametes and spores of the lower groups swim. Plantae includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms, which are the subject of the chapter on the plant kingdom.

The life cycle of plants has two distinct phases: the diploid sporophytic phase and the haploid gametophytic phase, which 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 generations. In algae and bryophytes the gametophyte dominates; in pteridophytes, gymnosperms and angiosperms the sporophyte dominates and the gametophyte is progressively reduced, until in angiosperms it is a few cells inside the flower.

Kingdom Animalia is characterised by heterotrophic eukaryotic organisms that are multicellular and whose 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 (determinate growth). Higher forms show elaborate sensory and neuromotor mechanisms. Most of them are capable of locomotion. The sexual reproduction is by copulation of male and female followed by embryological development. Animalia includes the sponges, cnidarians, worms, molluscs, arthropods, echinoderms and chordates, treated in the zoology course.

The five-kingdom classification, then, separates the two multicellular kingdoms of producers and consumers by the presence of cellulose walls, chloroplasts and starch on the one hand and the absence of walls, holozoic nutrition, glycogen and locomotion on the other. Fungi stand between them as absorptive consumers with chitin walls. The three represent the three ways of making a living that multicellular life discovered: photosynthesis, absorption and ingestion.

A comparison table of Plantae and Animalia is a frequent short question. Plantae: cellulose wall, chloroplasts, autotrophic, starch, non-motile, indeterminate growth, alternation of generations. Animalia: no wall, no plastids, heterotrophic holozoic, glycogen, motile, determinate growth, diploid life cycle with gametic meiosis.

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

Viruses. All of us have suffered from the ill effects of common cold or flu; viruses cause them. Viruses did not find a place in classification since they are not truly 'living', if we understand living as those organisms that have a cell structure. 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. They are therefore obligate intracellular parasites, at the boundary of the living and the non-living.

The name virus means venom or poisonous fluid, given by Pasteur. D. J. Ivanowsky (1892) recognised certain microbes as the 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. Beijerinck (1898) demonstrated that the extract of the infected plants of tobacco could cause infection in healthy plants and called the fluid Contagium vivum fluidum, infectious living fluid. W. M. Stanley (1935) showed that viruses could be crystallised and that crystals consist largely of proteins; he obtained the tobacco mosaic virus in crystalline form.

Structure. Viruses are made of protein and genetic material, which is either RNA or DNA, never both. 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 the capsid, made of small subunits called capsomeres, protects the nucleic acid. These capsomeres are arranged in helical or polyhedral geometric forms. Tobacco mosaic virus is a rod of helically arranged capsomeres around a single-stranded RNA; the T4 bacteriophage has a polyhedral head, a tail sheath and tail fibres; many animal viruses have an outer lipid envelope taken from the host membrane.

Diseases. Viruses cause diseases like mumps, smallpox, herpes, influenza, polio, rabies, AIDS (HIV), COVID-19 and dengue in humans; foot-and-mouth disease in cattle. In plants the symptoms can be mosaic formation, leaf rolling and curling, yellowing and vein clearing, dwarfing and stunted growth: tobacco mosaic, tomato leaf curl, bhendi yellow vein mosaic and papaya ring spot are common in Telangana fields.

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, a few hundred nucleotides, circular and single-stranded, coding for no protein. Viroids are known only in plants.

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, and these agents are called prions. The most notable diseases caused by prions are bovine spongiform encephalopathy (BSE), commonly called mad cow disease, and its analogous variant Creutzfeldt–Jacob disease (CJD) in humans. Prions contain no nucleic acid at all; the misfolded protein converts normal protein of the host into its own shape.

Lichens are symbiotic associations, mutually useful associations, between algae and fungi. The algal component is known as the phycobiont and the fungal component as the mycobiont, which are autotrophic and heterotrophic respectively. Algae prepare food for fungi, and fungi provide shelter and absorb mineral nutrients and water for their partner. 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. The lichen body, called a thallus, has a form and chemistry that neither partner shows alone, and lichens have long been named and classified as if they were single species.

Composition. The mycobiont is usually an ascomycete, rarely a basidiomycete; it makes up most of the thallus. The phycobiont is a green alga (commonly Trebouxia) or a cyanobacterium (commonly Nostoc), and some lichens contain both. In a section of the thallus the fungal hyphae form a compact upper cortex, an algal layer beneath it where the algal cells are enmeshed by hyphae, a loose medulla, and often a lower cortex with rhizines that attach the thallus. Where the phycobiont is a cyanobacterium the lichen also fixes nitrogen.

Forms. Three growth forms are recognised: crustose lichens form a crust tightly stuck to rock or bark, as if painted on (Graphis, Lecanora); foliose lichens are leaf-like, lobed and attached loosely by rhizines (Parmelia, Physcia); fruticose lichens are shrubby, branched and erect or hanging (Usnea, the old man's beard, and Cladonia, the reindeer moss).

Reproduction. Lichens reproduce vegetatively by fragmentation and by special propagules, soredia (small clusters of algal cells wrapped in hyphae, produced in powdery masses) and isidia (finger-like outgrowths of the thallus), which carry both partners together. The fungus alone also reproduces sexually, forming apothecia with asci and ascospores, which must find a suitable alga on germination.

Ecology and uses. Lichens grow very slowly, a few millimetres a year, and live for centuries on bare rock, tree bark, soil and even tombstones, in the Arctic, the desert and the high Himalaya. They are pioneers of rock surfaces, secreting acids that weather the rock and prepare soil for mosses and higher plants, the first step of ecological succession. Lichens are very good pollution indicators: they do not grow in polluted areas, because their unprotected thallus absorbs sulphur dioxide and heavy metals from the air, and the disappearance of lichens from a city marks the spread of its pollution. They are eaten by reindeer and caribou; some are used as food (the Indian 'stone flower' or rock moss used as a spice in Hyderabadi cooking is a lichen, Parmotrema); dyes such as orchil and the pH indicator litmus are extracted from Roccella; perfumes use oak moss (Evernia); and lichen acids such as usnic acid are antibiotic.

The examination asks for the definition of a lichen, the names of the two components with their roles, and one use, most often as pollution indicators. Students should not confuse lichen with mycorrhiza, which is also a fungus–plant symbiosis but occurs on roots of higher plants and has no alga.