Biological Classification

Linnaeus divided the living world into two kingdoms, Plantae and Animalia, and for a long time that was enough. It matched what people could see. Things that were green and stayed still were plants; things that moved and ate were animals.

The microscope broke the system. Once biologists could see single-celled organisms, the two boxes stopped working. Where does a bacterium go? It has a cell wall, which sounds plant-like, but no chlorophyll and no nucleus. Where does Euglena go? It photosynthesises in the light like a plant, and swims with a flagellum and feeds on other organisms in the dark like an animal. A fungus has a cell wall and does not move, so botanists took it — but it has no chlorophyll at all and absorbs its food ready-made, which is nothing like a plant does.

These are not exotic edge cases. They are enormous groups of organisms, and the two-kingdom system had no honest place for any of them. The deeper problem is that the system used the wrong criteria. Being green and being still are descriptions of appearance. They say nothing about how a cell is built, how the organism gets energy, or what it is related to.

Several attempts were made to patch this. Haeckel proposed a third kingdom, Protista, for the single-celled organisms that fitted neither box. Copeland separated the organisms without a true nucleus into their own kingdom. Each fix helped, and each still left something awkward.

The change that stuck came in 1969, when R.H. Whittaker proposed a five-kingdom system. What made it work was not that it had more boxes, but that it chose better criteria for drawing the lines.

Whittaker used five criteria: cell structure, body organisation, mode of nutrition, mode of reproduction, and phylogenetic relationships. The order matters when you are placing an organism, because the first criterion does most of the work.

Cell structure asks a single question: does the cell have a true nucleus bounded by a membrane, and membrane-bound organelles? If it does not, the organism is prokaryotic and goes to Monera, whatever else is true of it. This one distinction separates one kingdom from the other four.

Body organisation asks whether the organism is unicellular, colonial, filamentous or multicellular with tissues. Mode of nutrition asks how it obtains organic food: autotrophic if it makes its own by photosynthesis or chemosynthesis, heterotrophic if it takes it ready-made — and heterotrophs divide further into those that absorb dissolved food (saprophytes and parasites) and those that ingest solid food. Mode of reproduction and phylogenetic relationships refine the placement further.

The five kingdoms that result are Monera, Protista, Fungi, Plantae and Animalia. Applying the criteria in order: all prokaryotes go to Monera. Among the eukaryotes, the single-celled ones go to Protista. Of the rest, those that absorb their food go to Fungi, those that photosynthesise go to Plantae, and those that ingest their food go to Animalia. The rule about single cells is a guide rather than a hard line — yeasts are unicellular and still sit in Fungi, because their nutrition, their cell wall and their way of reproducing place them with the other fungi.

The system is a large improvement, but it is not perfect, and the textbook says so. Protista in particular remains an awkward kingdom — the boundaries between its groups, and between Protista and the kingdoms above it, are still debated. A classification is a tool for organising knowledge, not a law of nature, and it changes as the knowledge does.

Monera contains all prokaryotes — organisms whose cells have no membrane-bound nucleus and no membrane-bound organelles. They are the most abundant organisms on the planet and occur in nearly every habitat that has been examined.

By shape, bacteria fall into four types: spherical coccus, rod-shaped bacillus, comma-shaped vibrio and spiral spirillum. Shape is the easiest feature to see under a microscope, but it says little about how the organism lives — two bacteria of the same shape may feed in completely different ways.

Archaebacteria live in conditions that would destroy most cells: salt-saturated water (halophiles), hot springs (thermoacidophiles), and marshy areas and the guts of ruminant animals such as cows and buffaloes (methanogens, which produce methane from the dung of these animals). What allows this is a cell wall of a different chemical construction from other bacteria — the structural detail that also marks them as a distinct lineage.

Eubacteria, the true bacteria, are characterised by a rigid cell wall and, if motile, a flagellum. Within them, the cyanobacteria or blue-green algae are photosynthetic autotrophs with chlorophyll a, occurring singly or in colonies held together by a gelatinous sheath. Some of the filamentous forms produce specialised thick-walled cells called heterocysts, spaced along the filament, and it is inside these cells that atmospheric nitrogen is fixed. Other eubacteria are chemosynthetic autotrophs, oxidising inorganic substances such as nitrates, nitrites and ammonia and using the released energy to make their own food — a group that plays a large part in recycling nutrients.

The majority of bacteria, however, are heterotrophs that absorb their food. Many are decomposers, and their role in nature is enormous: they return the elements locked in dead material back to the soil. Others are used in making curd from milk, in producing antibiotics, and in fixing nitrogen in the root nodules of legumes.

Mycoplasma are the smallest living cells known, and they have no cell wall at all. They can survive without oxygen.

Bacteria reproduce mainly by binary fission, and under unfavourable conditions many form spores. They also reproduce by a sort of sexual reproduction in which DNA is transferred from one bacterium to another.

Protista contains all single-celled eukaryotes. Because that definition sweeps together organisms with very different ways of living, the boundaries within the kingdom are not settled, and what one biologist includes another may not. The textbook is explicit that this is an unsatisfactory group.

Chrysophytes include the diatoms and desmids. They are found in fresh and marine water, are microscopic, and float passively. Diatoms have a cell wall in two overlapping halves that fit together like a soap-box, and the walls are embedded with silica, so they do not decay. Over long periods their remains pile up as diatomaceous earth, which is used in polishing and in filtration. Diatoms are the chief producers in the oceans.

Dinoflagellates are mostly marine and photosynthetic. Their colour depends on the pigments present — yellow, green, brown, blue or red. The cell wall carries stiff cellulose plates on the outer surface. Most have two flagella that beat in different directions: one runs lengthwise along the body, from front to back, while the other lies crosswise around the cell, sitting in a groove that runs between the plates like a belt. The lengthwise one drives the cell forward and the crosswise one spins it, which is why these organisms move with a whirling motion. Rapid multiplication of red dinoflagellates such as Gonyaulax can make the sea appear red, the phenomenon called a red tide.

Euglenoids are mostly freshwater organisms found in stagnant water. Instead of a cell wall they have a protein-rich layer called a pellicle, which makes the body flexible. They have two flagella, one short and one long. Photosynthetic in sunlight, they feed on smaller organisms when deprived of light — which is exactly the dual behaviour that broke the two-kingdom system.

Slime moulds are saprophytic protists. The body moves along decaying material, engulfing organic matter. Under suitable conditions they form an aggregation called a plasmodium, which may grow and spread over several feet. During unfavourable conditions the plasmodium differentiates and forms fruiting bodies bearing spores, and the spores possess true walls and are extremely resistant, surviving for many years.

Protozoans are all heterotrophs, living as predators or parasites, and are believed to be primitive relatives of animals. There are four major groups: amoeboid protozoans, which move and capture prey by pseudopodia; flagellated protozoans, which have flagella; ciliated protozoans, which have thousands of cilia and a cavity or gullet that opens to the outside, with the coordinated movement of cilia steering water laden with food into the gullet; and sporozoans, which have an infectious spore-like stage in their life cycle.

Fungi are heterotrophic eukaryotes that absorb dissolved organic matter through their cell walls. They are cosmopolitan, occurring in air, water, soil and on animals and plants. They prefer warm and humid places, which is why bread left out in the monsoon grows mould so readily.

With the exception of yeasts, which are unicellular, fungi are filamentous. The body consists of long, slender thread-like structures called hyphae, and the network of hyphae is called a mycelium. Some hyphae are continuous tubes filled with multinucleated cytoplasm — these are coenocytic hyphae. Others have septa or cross walls. The cell walls are composed of chitin and polysaccharides.

Most fungi are saprophytes, absorbing from dead substrates. Some are parasites. Others live in symbiotic association: with algae as lichens, and with the roots of higher plants as mycorrhiza.

Reproduction is by vegetative means — fragmentation, fission and budding — and asexually by spores called conidia, sporangiospores or zoospores. Sexual reproduction proceeds by oospores, ascospores and basidiospores, produced in distinct structures called fruiting bodies. The sexual cycle has three steps: fusion of protoplasms between two motile or non-motile gametes, called plasmogamy; fusion of two nuclei, called karyogamy; and meiosis in the zygote, resulting in haploid spores. In some fungi the two haploid nuclei do not fuse immediately but stay as a pair, giving a stage called dikaryon, and the parental nuclei fuse later.

The four classes are separated by the way spores are formed. Phycomycetes occur in aquatic habitats and on decaying wood, and their asexual spores are produced in a sporangium. Ascomycetes, the sac fungi, produce ascospores inside sac-like asci. Basidiomycetes, which include mushrooms and puffballs, produce basidiospores externally on a club-shaped basidium. Deuteromycetes are known as the imperfect fungi because only their asexual phase is known; when the sexual form of a member is discovered, it is moved to the appropriate class.

Plantae includes all eukaryotic, chlorophyll-containing organisms — the plants. Most are autotrophic, making their own food by photosynthesis, though a few are partly heterotrophic. The insectivorous plants such as bladderwort and Venus flytrap trap and digest insects while still photosynthesising; the parasite Cuscuta has lost its chlorophyll altogether and draws its nutrition from the host plant it grows on. These are kept in Plantae because they are built as plants and descend from plants — a reminder that the kingdom's description fits most of its members rather than every one of them.

The plant cell has a cell wall composed mainly of cellulose — a useful contrast with the chitin wall of fungi and the absence of a wall in animal cells. The plant life cycle shows alternation of generations: a haploid gametophyte phase alternates with a diploid sporophyte phase, and the two differ in length and dominance across the plant groups.

Animalia includes heterotrophic, multicellular eukaryotes whose cells lack a cell wall. They obtain food by ingestion — taking in solid material and digesting it in an internal cavity — and store carbohydrate as glycogen or as fat. This holozoic mode of nutrition is what separates them from the fungi, which absorb food already dissolved.

Animals have a definite growth pattern, reaching an adult form after which growth stops, and most have sensory and neuromotor mechanisms allowing them to move. Reproduction is mostly sexual, by the fusion of male and female gametes.

It is worth noticing what happened to the two original kingdoms. They still exist, but they are no longer defined by appearance. A plant is now a multicellular eukaryote that photosynthesises; an animal is a multicellular eukaryote that ingests. The definitions rest on cell structure and nutrition, exactly the criteria the old system lacked.

Whittaker's system classifies cellular organisms. Some entities are not cellular at all, and the textbook places them outside the five kingdoms rather than forcing them in. Understanding why they are excluded teaches you what the system is actually built on.

Viruses are not included because they are not strictly living organisms. A virus is inert outside a host cell — it does not respire, grow, or reproduce on its own — and becomes active only inside one. This is why the name means venom or poisonous fluid, and why viruses are often described as being on the boundary of the living and the non-living.

Structurally, a virus is a nucleoprotein: genetic material surrounded by a protein coat called a capsid, made of subunits called capsomeres. The genetic material can be RNA or DNA, but never both in the same virus — one or the other. In general, viruses that infect plants have single-stranded RNA, and those that infect animals have either single- or double-stranded RNA or double-stranded DNA. A bacterial virus, called a bacteriophage, usually has double-stranded DNA. The protein coat protects the genetic material.

Some historical names go with this. D.J. Ivanowsky recognised the agent of tobacco mosaic disease, and M.W. Beijerinck demonstrated that an extract could cause the same effect in healthy plants, calling the fluid contagium vivum fluidum. W.M. Stanley later showed that these could be crystallised — a property no cellular organism has, and a strong hint that they are not organisms in the ordinary sense.

Viroids go further still. Discovered by T.O. Diener, a viroid is free RNA without the protein coat, and of lower molecular weight than viral RNA. If a virus is a minimal thing, a viroid is smaller again.

Prions are stranger. They are abnormally folded proteins, similar in size to viruses, with no genetic material at all. An infectious agent made only of protein, with no nucleic acid, was so unexpected that it required a rethink of what could transmit a condition.

Lichens are excluded for the opposite reason: they are not one organism but two. A lichen is a symbiotic association between an alga and a fungus. The algal component, the phycobiont, is autotrophic and prepares food; the fungal component, the mycobiont, is heterotrophic and provides shelter and absorbs mineral nutrients and water. The relationship is so close that a lichen looks like a single organism, and it cannot be placed in a system that assumes one organism per name. Lichens are also good pollution indicators — they do not grow in polluted areas.