Biological Classification: Class 11 Biology · Chapter 2

Walk through a sabzi mandi and you will see sorting everywhere: leafy greens in one heap, gourds in another, onions and potatoes kept dry at the back. The grouping serves the seller and the cook, not the biologist. For thousands of years people sorted living things in just this way, by what they gave us as food, shelter or clothing, long before anyone asked how organisms are built or how they are related.

From two kingdoms to five

Aristotle, in ancient Greece, made the earliest attempt to sort life by its own features rather than its uses. Plants he called trees, shrubs or herbs according to their overall form; animals he split by whether or not they had red blood. Both are simple morphological characters: features of outward form that you can see without cutting the organism open.

About two thousand years later, in Linnaeus's time, naturalists settled on a two-kingdom system: every organism was either a plant (Plantae) or an animal (Animalia). It was easy to teach, but it lumped together organisms that differ in fundamental ways. Cells without a true nucleus sat beside cells with one; single cells sat beside many-celled bodies; and green algae that photosynthesise shared a kingdom with fungi that cannot. Plenty of organisms fitted neither box comfortably (Fig. 2.1).

Two kingdoms gave way to three, four and eventually five as biologists began to weigh characters hidden from the naked eye: how the cell is built, what its wall is made of, how the organism feeds, where it lives, how it reproduces and whom it descends from. Through every revision Plantae and Animalia survived as kingdoms, although what counted as a plant or an animal kept shifting; the number and nature of the remaining kingdoms changed most of all.

In 1969 the American ecologist R.H. Whittaker proposed a five-kingdom classification: Monera, Protista, Fungi, Plantae and Animalia. He sorted organisms by five criteria:

• cell structure: prokaryotic or eukaryotic;
• body organisation: single cells, loose tissue, or tissues and organs;
• mode of nutrition: making food (autotrophic) or obtaining it ready-made (heterotrophic);
• reproduction;
• phylogenetic relationships, that is, evolutionary ancestry.

Ask what a mushroom, a moss and a bacterium have in common, and the old answer was: a cell wall. That one shared character was enough to file flowering plants, gymnosperms, ferns and mosses together with fungi, blue-green algae and bacteria as 'plants'. Look closer and the group falls apart in three ways:

• Nucleus: bacteria and blue-green algae are prokaryotes, with no true nucleus; everything else in the group is a eukaryote.
• Number of cells: single-celled algae sat beside many-celled ones.
• Food and walls: fungi absorb ready-made food and build walls of chitin; green plants make their own food and build walls of cellulose.

Whittaker's answer was to give each kind of organisation its own kingdom: Monera for every prokaryote, Fungi for the chitin-walled absorbers and Protista for single-celled eukaryotes, leaving Plantae and Animalia for the many-celled producers and consumers. One side effect surprises students. Walled, photosynthetic single cells once filed among the algae now share Protista with wall-less, food-engulfing cells such as Amoeba that used to be called animals. The organisms had not changed; the rules had.

No classification is final. Each new tool, from the electron microscope to DNA sequencing, reveals characters that can redraw the lines, and the aim today is a phylogenetic system, one that mirrors the real branching history of life and not just shared structure, physiology and reproduction. One such redraw, the three-domain system, splits Monera into two domains and puts all eukaryotes in a third, giving six kingdoms in all.11The domains Bacteria, Archaea and Eukarya were proposed by Carl Woese and his colleagues in 1990. You will meet them in higher classes; this book follows Whittaker. This chapter treats Monera, Protista and Fungi in detail and sketches Plantae and Animalia, which Chapters 3 and 4 cover.

Whittaker's criteria can be turned into a short key, a chain of yes-or-no questions that ends at one kingdom (Fig. 2.2). Table 2.1 sets the same characters side by side.

2.1 Kingdom Monera

Scoop up a gram of fertile garden soil and you may be holding hundreds of millions of bacteria. They are the most abundant organisms on Earth and the only members of Monera. Few places are too harsh for them: hot springs, salt pans, deserts, polar snow and the deep sea floor all have their bacteria, and many kinds live on or inside plants and animals, some harmlessly and some as parasites.

Under a microscope bacteria show four basic shapes (Fig. 2.3): spheres (coccus, plural cocci), rods (bacillus, plural bacilli), commas (vibrio) and spirals (spirillum, plural spirilla).22NCERT writes the comma form's singular as vibrium and its plural as vibrio; most microbiology books call one cell a vibrio and many cells vibrios. Shape is one of the first things a microbiologist records about an unknown bacterium.

Simple bodies hide remarkable chemistry. Between them, bacteria can live on sunlight, on inorganic chemicals or on almost any organic food; no other group shows such wide metabolic diversity. Autotrophic bacteria build their food from inorganic raw materials, powered by light (photosynthetic autotrophs) or by energy from chemical reactions (chemosynthetic autotrophs). Most bacteria, though, are heterotrophs that live on food made by other organisms, living or dead.

2.1.1 Archaebacteria

Archaebacteria owe their toughness to a cell wall unlike that of any other bacterium, and it lets them colonise places that would kill most cells (Fig. 2.4). Each group is named after its extreme: halophiles ('salt-lovers') in brine, thermoacidophiles ('heat-and-acid-lovers') in hot, acidic springs, and methanogens ('methane-makers') in marshy mud.

Methanogens also live in the gut of ruminants such as cows and buffaloes. Because the animals' dung carries them, dung left to ferment in a closed tank releases biogas, a fuel that is mostly methane.

2.1.2 Eubacteria

The thousands of remaining kinds are eubacteria, the 'true bacteria'. A rigid cell wall surrounds each cell, and those that swim are driven by a flagellum.

Among eubacteria the cyanobacteria (blue-green algae) come closest to plants: they photosynthesise with chlorophyll a, the pigment green plants use. You find them wherever it is wet or damp, in ponds, in the sea and on moist soil, as single cells, as colonies held in a gelatinous sheath, or as filaments. Some filamentous kinds, such as Nostoc and Anabaena, also fix atmospheric nitrogen inside special thick-walled cells called heterocysts (Fig. 2.5). When a pond or lake is enriched with sewage or fertiliser runoff, cyanobacteria can multiply into a dense green bloom.

Some eubacteria make food in total darkness. These chemosynthetic autotrophs draw energy by oxidising inorganic substances such as ammonia and nitrite, and they capture that energy as ATP. In the process they help recycle nutrients such as nitrogen, phosphorus, iron and sulphur through ecosystems.

The heterotrophic bacteria outnumber all the rest. Without them dead leaves and bodies would pile up, because most are decomposers (saprophytes) that return the minerals locked in dead matter to the soil. Our lives are tangled with theirs: the curd in your kitchen, many antibiotics and the nitrogen-fixing nodules on the roots of gram and moong are all their work. Others are pathogens. Cholera, typhoid and tetanus in people and citrus canker in lemon and orange orchards are bacterial diseases, and other species attack crops, farm animals and pets.

A bacterium's usual way to multiply is fission: it copies its DNA, grows and splits into two daughter cells (Fig. 2.6); in ideal conditions some kinds divide every 20 minutes or so. Hard times trigger a different response, and many bacteria form resistant spores. Bacteria also show a primitive kind of sexual reproduction, in which DNA passes from one bacterium to another.

Mycoplasmas hold two records among bacteria: they have no cell wall at all, and they are the smallest living cells known. They can live without oxygen, and many are pathogens of plants and animals.

2.2 Kingdom Protista

Protista is the kingdom for eukaryotes that never went beyond a single cell. Its borders are argued over (is a photosynthetic one-celled alga a protist or a plant? biologists disagree), so books differ in what they include. Here it holds five groups, most of them aquatic: chrysophytes, dinoflagellates, euglenoids, slime moulds and protozoans.

Inside, a protist is a complete eukaryotic cell, with a nucleus enclosed by a membrane and other membrane-bound organelles. Many swim with flagella or cilia. Besides reproducing asexually, protists reproduce sexually when two cells fuse into a zygote. Some look plant-like, some animal-like and some fungus-like, so Protista is often described as the link between those three kingdoms.

2.2.1 Chrysophytes

Drifting in every pond and ocean are countless microscopic organisms that cannot swim against the current: the plankton. Many are chrysophytes, a group made up of the diatoms and the golden algae (desmids).33Most phycologists today place desmids among the green algae; for exams, follow NCERT's grouping. Chrysophytes live in fresh water and in the sea alike, and most photosynthesise. Diatoms matter enormously: they are the chief producers of the oceans, the base on which much of marine life depends.

A diatom lives inside a glassy box. Its wall consists of two thin halves, one slightly larger, that overlap like a lid on its base (Fig. 2.7). The walls are impregnated with silica, so they do not decay. Over millions of years the shells of dead diatoms have piled up on lake and sea floors as thick deposits called diatomaceous earth, a gritty powder used for polishing and for filtering oils and syrups.

2.2.2 Dinoflagellates

Now and then a stretch of coastal sea turns red. The cause is a red tide: red dinoflagellates such as Gonyaulax multiplying so fast that they colour the water, and releasing toxins in such quantity that fish and other marine animals die.

Dinoflagellates are mostly marine, photosynthetic protists whose colour, yellow, green, brown, blue or red, depends on their main pigments. Stiff cellulose plates armour the outer surface of the wall. Most have two flagella: one lies across the cell in a groove between the plates, and the other runs along its length (Fig. 2.8).

2.2.3 Euglenoids

Keep a jar of pond water containing Euglena in a dark cupboard and the cells do not starve. Euglenoids photosynthesise in sunlight but, deprived of light, switch to heterotrophic feeding and prey on smaller organisms (Fig. 2.9). Strikingly, their pigments are the same as those of higher plants. Most euglenoids live in stagnant fresh water. They have no cell wall; a protein-rich layer, the pellicle, keeps the body flexible, and each cell bears two flagella, a short one and a long one.

2.2.4 Slime Moulds

On a damp forest floor you may find a slimy yellow film creeping over a rotting log: a slime mould, one of the saprophytic protists. It feeds by engulfing the organic matter of decaying twigs and leaves. While food and moisture last, the cells gather into a plasmodium, a mass that can spread over several feet (Fig. 2.10). When conditions turn bad, the plasmodium rebuilds itself into fruiting bodies tipped with spores. The spores have true walls and are extremely resistant, staying alive for many years, and air currents carry them away.

2.2.5 Protozoans

Protozoans are the animal-like protists, believed to be primitive relatives of animals. Every one of them is a heterotroph, hunting as a predator or living as a parasite. Biologists recognise four major groups (Fig. 2.11):

• Amoeboid protozoans (fresh water, sea water, damp soil) push out pseudopodia, or 'false feet', both to crawl and to surround prey; Amoeba is the classic case. Marine species carry silica shells, and Entamoeba lives as a parasite in the human gut.
• Flagellated protozoans swim by beating flagella. Some are free-living; parasitic ones include Trypanosoma, spread by the tsetse fly, which causes sleeping sickness.
• Ciliated protozoans such as Paramoecium are covered with thousands of cilia and swim actively. Coordinated waves of cilia drive water, and the food in it, into the gullet, a cavity that opens at the cell surface.
• Sporozoans pass through an infectious, spore-like stage. The most notorious is Plasmodium: spread by female Anopheles mosquitoes, it causes malaria, which still kills hundreds of thousands of people every year.

2.3 Kingdom Fungi

Leave a slice of bread or a cut guava out during the monsoon and within days it wears a fuzzy coat: a fungus. Fungi are a kingdom of heterotrophs found in an astonishing range of shapes and places. Some feed us or work for us: the mushrooms in the market, yeast (a single-celled fungus) that raises bread dough and ferments beer, and Penicillium, a source of antibiotics. Others are rivals: toadstools are inedible, a parasitic fungus causes the white spots on mustard leaves, and Puccinia causes the rust disease of wheat.

Fungal spores ride on air and water and settle on soil, plants and animals, so fungi are cosmopolitan. Warmth and humidity suit them best. That is why leather shoes grow mould in the monsoon, and why a refrigerator, by keeping food cold, slows its spoiling by fungi and bacteria.

Look at the fuzz through a hand lens and you will see threads. Each thread is a hypha, and the tangled network of hyphae is a mycelium (Fig. 2.12); only the yeasts break the pattern by living as single cells. Hyphae come in two designs. Coenocytic hyphae are continuous tubes with many nuclei scattered through the cytoplasm, while in septate hyphae cross walls called septa divide the tube into compartments. Either way, the walls are made of chitin together with other polysaccharides.

Fungi never ingest food; they absorb it. Most absorb soluble organic matter from dead substrates such as fallen leaves and rotting wood, and are therefore saprophytes. Parasitic fungi absorb it from living plants and animals. Symbiotic fungi trade with a partner: an alga in a lichen (Lichens), or the roots of a higher plant in mycorrhiza.

Spores are how fungi spread, and they come in several kinds. Asexual spores are conidia, sporangiospores or zoospores; sexual spores are oospores, ascospores or basidiospores; and both are borne on or in special structures, the fruiting bodies. Fungi can also multiply vegetatively, by fragmentation, fission or budding.

In sexual reproduction, two haploid hyphae of compatible mating types meet and fuse. The cycle then runs through three steps (Fig. 2.13):

1. Plasmogamy: the protoplasm of two gametes, motile or non-motile, fuses.
2. Karyogamy: their two nuclei fuse.
3. Meiosis in the zygote produces haploid spores.

Fungi differ in the gap between the two fusions. If karyogamy follows plasmogamy immediately, the cells become diploid (2n) at once. Ascomycetes and basidiomycetes pause instead: for a time each cell carries two separate parental nuclei, a condition called a dikaryon (n + n), and this stretch of the life cycle is the dikaryophase. Eventually the nuclei fuse, and meiosis inside the fruiting body returns the fungus to haploid spores.

Three features divide the kingdom into classes: the form of the mycelium, the way spores are produced, and the type of fruiting body. Four classes are recognised here.

2.3.1 Phycomycetes

Mucor, Rhizopus (the bread mould of the activity above) and Albugo, which causes the white spots on mustard leaves, are phycomycetes. Members of this class live in water, on damp decaying wood, or as obligate parasites of plants, and their mycelium is aseptate and coenocytic. Asexual spores develop inside a sporangium (endogenously): either zoospores, which swim, or aplanospores, which cannot. Sexual fusion of two gametes gives a zygospore; the gametes may look alike (isogamous) or differ (anisogamous or oogamous).

2.3.2 Ascomycetes

The ascomycetes take their common name, sac fungi, from the sac-like ascus (plural asci) in which their sexual spores, the ascospores, form (endogenously); the asci are packed into fruiting bodies called ascocarps. Asexually they produce conidia outside (exogenously) on special hyphae, the conidiophores, and each conidium can germinate into a new mycelium. The mycelium is branched and septate. Most ascomycetes are multicellular, like Penicillium, but yeast (Saccharomyces) is a single cell.

Ascomycetes live as saprophytes, decomposers or parasites, and some are coprophilous, growing on dung. Other examples are Aspergillus, Claviceps and Neurospora, a favourite organism of geneticists and biochemists. Some ascomycetes are delicacies: morels (the gucchi of Himalayan forests) and truffles fetch very high prices.

2.3.3 Basidiomycetes

Every basidiomycete is defined by its basidium (plural basidia): a club-shaped cell in which karyogamy and meiosis take place and on whose outside four basidiospores form (exogenously). Basidia are grouped in fruiting bodies called basidiocarps, such as the umbrella of a mushroom. Mushrooms, bracket fungi and puffballs are the familiar members, growing in soil and on logs and tree stumps; rusts and smuts are basidiomycetes that live as parasites inside living plants. Examples: Agaricus (the button mushroom), Ustilago (smut) and Puccinia (rust).

Their sexual cycle is unusual: there are no sex organs. Plasmogamy happens when two vegetative (somatic) cells of different strains or genotypes fuse, giving a dikaryotic mycelium that eventually produces basidia. Asexual spores are generally not formed, though the branched, septate mycelium often multiplies by fragmentation.

2.3.4 Deuteromycetes

Alternaria, Colletotrichum and Trichoderma belong to the deuteromycetes, or imperfect fungi. 'Imperfect' means that only their asexual or vegetative stages are known: they reproduce solely by conidia, and their mycelium is branched and septate. Some are saprophytes and some parasites, while many decompose leaf litter and keep minerals cycling.

The class is really a holding area. Once a member's sexual ('perfect') stage is discovered, the fungus moves to the class where it belongs, most often the ascomycetes or basidiomycetes. Sometimes a fungus's asexual stage carried one name and sat here while its sexual stage had a different name in another class; once the two were shown to be one organism, it left the deuteromycetes.

2.4 Kingdom Plantae

Algae, bryophytes, pteridophytes, gymnosperms and angiosperms together make up Kingdom Plantae: the chlorophyll-bearing eukaryotes we commonly call plants. Plant cells have prominent chloroplasts and walls made mainly of cellulose (Chapter 8 looks at cell structure in detail).

Not every plant lives by photosynthesis alone. Insectivorous plants such as the pitcher plant Nepenthes khasiana of Meghalaya, the sundews and the bladderworts also trap small animals for extra nitrogen, and Cuscuta (dodder, अमरबेल), whose yellow threads smother hedges, is a parasite that draws its food from a host plant. Such plants are partly heterotrophic.

A plant's life cycle switches between two generations, a pattern called alternation of generations (Fig. 2.16). The diploid sporophyte makes spores by meiosis; each spore grows into a haploid gametophyte, which makes gametes; gametes fuse, and the zygote grows into a new sporophyte. How long each generation lasts, and whether it lives independently or depends on the other, differs between plant groups; Chapter 3 compares them.

2.5 Kingdom Animalia

What makes an animal? Start with its food. Animals take food into the body and digest it in an internal cavity: holozoic nutrition. Ultimately that food comes from plants, eaten directly or through a food chain, and the surplus is stored as glycogen or fat. Animal bodies are multicellular and eukaryotic, and their cells have no cell wall.

Most animals can move from place to place, and the more complex ones have elaborate sense organs and neuromotor (nerve-and-muscle) systems. An animal grows by a definite pattern into an adult of definite shape and size, starting as an embryo produced by sexual reproduction in which a male and a female copulate. Chapter 4 surveys the animal phyla.

2.6 Viruses, Viroids, Prions and Lichens

Whittaker's five kingdoms leave out four things you will meet again and again in biology: lichens, and three acellular (non-cellular) agents, viruses, viroids and prions. This section introduces each one briefly.

Viruses

A virus outside a cell is about as lively as a grain of salt: it does nothing, and many viruses can be crystallised. Inside a suitable host cell it takes over the cell's machinery, makes copies of itself and usually kills the host; you have felt the result whenever you caught a cold or the flu. Because viruses are not cells, and 'living' is usually taken to mean 'made of cells', Whittaker gave them no kingdom. So are viruses living or non-living?

The word virus comes from the Latin for venom or poisonous fluid. A series of experiments on tobacco mosaic disease revealed what kind of agent it named (timeline). Viruses turned out to be obligate parasites: inert outside, they multiply only inside the living cells of a particular host.

Every virus is a nucleoprotein: a core of nucleic acid, the part that carries the infection, inside a coat of protein. The nucleic acid is RNA in some viruses and DNA in others, but never both, and which kind a virus carries tends to go with its host (Table 2.5).

The protein coat, or capsid, protects the nucleic acid. It is assembled from many small subunits called capsomeres, arranged either as a helix, which gives a rod like tobacco mosaic virus, or as a polyhedron, like the many-faced head of a bacteriophage (Fig. 2.18).

Name a viral disease and you might list mumps, smallpox (now eradicated), herpes, influenza or AIDS. In crops a virus announces itself through the leaves: a mottled mosaic of light and dark green, leaves that roll or curl, yellowing, veins that turn pale (vein clearing), and plants that stay dwarf and stunted.

Viroids

Imagine an infectious agent that is nothing but a short strand of RNA, with no protein coat at all. That is a viroid ('virus-like'), discovered in 1971 by T.O. Diener as the cause of potato spindle tuber disease. Its RNA is of low molecular weight, and the whole agent is smaller than any virus.

Prions

Bovine spongiform encephalopathy (BSE), better known as mad cow disease, and its human counterpart Creutzfeldt–Jakob disease (CJD) are infectious diseases of the nervous system with a strange cause: an agent made only of abnormally folded protein, with no nucleic acid, about the size of a virus.44NCERT spells the second name Jacob; the disease is named after the German neurologists Hans Gerhard Creutzfeldt and Alfons Maria Jakob. Such agents are called prions.

Lichens

The grey-green crusts and leafy patches on old walls and tree trunks look like single organisms, but each lichen is two: a fungus and an alga living in a symbiotic partnership that benefits both (Fig. 2.19). The fungal partner, the mycobiont, is heterotrophic; it shelters the alga and absorbs water and mineral nutrients for both. The algal partner, the phycobiont, is autotrophic; it photosynthesises and shares the food it makes.

Lichens are very sensitive to air pollution, especially to sulphur dioxide, and do not grow in polluted areas. That makes them excellent pollution indicators: trunks thick with lichens are a sign of clean air.