The five kingdoms, species concepts and viruses

Five kingdoms, feature by feature

A kingdom is identified by a set of features covering cellular organisation, the material of the cell wall, the method of nutrition and the carbohydrate storage product. Those features place an unfamiliar organism; a list of example organisms does not. Prerequisite: classification, phylogeny and molecular evidence.

The scheme is Robert Whittaker's five kingdoms of 1969, and its first division is on cellular organisation. Prokaryotae have no nucleus. Their DNA is circular and lies free in the cytoplasm rather than being wrapped in a nuclear envelope, they have no membrane-bound organelles of any kind, their ribosomes are the smaller 70S type, and the wall of a bacterium is made of peptidoglycan, which is a polymer of sugars cross-linked by short peptides and is found nowhere else in nature. That feature is specific in both directions: archaea build their walls from other materials, so peptidoglycan identifies a bacterium rather than every member of this kingdom. They are unicellular, usually a few micrometres across, and they divide by binary fission rather than by mitosis. They feed in every way there is: absorbing organic material, photosynthesising, and in some cases oxidising inorganic molecules such as ammonium, which is what the nitrifying bacteria of the nitrogen cycle are doing.

Protoctista is defined by exclusion. Its members are eukaryotes, so they have a nucleus and membrane-bound organelles, and the definition is negative: a eukaryote that is not a fungus, a plant or an animal. Most are unicellular, such as Amoeba, Paramecium and Plasmodium; some are large and multicellular, such as the seaweeds, which are kept out of the plant kingdom because they lack roots, stems, leaves and the tissues that go with them. Some photosynthesise, some ingest food, some absorb it, and some do more than one. Cell walls are present in some and absent in others. A grouping this mixed is not a natural one, and modern classifications have broken it into several kingdoms; it survives at A level because the specifications still name it.

Fungi are eukaryotic and are built either as single cells, as in yeasts, or as long threads called hyphae that spread into a network called a mycelium. The hyphae are often not divided into separate cells at all, so a length of hypha can contain many nuclei in shared cytoplasm. The wall is made of chitin, not cellulose, and the wall material separates a fungus from a plant. No fungus photosynthesises. They feed saprotrophically, by secreting enzymes onto dead organic matter and absorbing the soluble products, or parasitically by doing the same to a living host, and they store carbohydrate as glycogen rather than as starch. They reproduce by spores, which are produced in enormous numbers and carried on the wind.

Plantae are multicellular eukaryotes whose cells have a wall of cellulose, a large permanent central vacuole, and, in the tissues exposed to light, chloroplasts containing chlorophyll. They are autotrophic: they make their own organic molecules by photosynthesis and store carbohydrate as starch. They do not move from place to place, they are differentiated into tissues and organs, and the ones you meet most have roots, stems and leaves with vascular tissue running through them.

Animalia are multicellular eukaryotes with no cell wall, so their cells can change shape. They are heterotrophic and, unlike fungi, they ingest their food, taking it inside the body and digesting it there, usually in a gut. They store carbohydrate as glycogen. Nearly all move at some stage of the life cycle, and nearly all have nervous coordination, which the other four kingdoms lack.

Kingdom

The largest of the taxonomic groups within a domain, and the level at which organisms are separated by features such as the presence of a nucleus, the material of the cell wall and the method of nutrition.

Saprotrophic nutrition

Feeding by secreting enzymes onto dead organic material outside the body and absorbing the soluble products, which is how fungi and many bacteria feed.

Autotroph

An organism that makes its own organic molecules from inorganic ones, in almost all cases by photosynthesis.

Heterotroph

An organism that obtains organic molecules by consuming other organisms or their remains.

The traditional five-kingdom model groups organisms as Prokaryotae, Protoctista, Fungi, Plantae and Animalia. Molecular evidence later separated prokaryotes into the domains Bacteria and Archaea; the other four traditional kingdoms lie within Eukarya. The two schemes use different ranks and are not directly interchangeable. Both are taxonomic systems, and modern classification aims to reflect evolutionary relationships.

Exam-board note: OCR Biology A requires the five-kingdom features and the three domains, so both schemes are examinable.

Three species concepts

More than one definition of a species is in use, because no single definition can be applied to every organism. Cambridge International names three, and a question can ask for any of them.

The biological species concept is the one to give first: a group of organisms with similar characteristics that can breed with one another to produce fertile offspring, and which are reproductively isolated from other such groups. Give both halves of the definition. The concept identifies a biological boundary, the gene pool: members of one species exchange alleles and members of two species do not. Its limitations are all of the same kind. The interbreeding test cannot be applied to an organism that reproduces asexually, cannot be applied to a fossil, and does not resolve cases where two named species produce fertile hybrids.

The morphological species concept groups organisms by observable structure: individuals that look alike, in the features a specialist counts as important, are put in one species. This is what Linnaeus did, it is what a field guide uses, and it is the only concept available for fossils and for museum specimens. Its weakness is that structure can mislead in both directions. Members of one species can look very different, as male and female birds of many species do, and as a caterpillar and a butterfly do; and two genuinely separate species can look nearly identical, which is what cryptic species are, and several mosquito species that differ in whether they carry malaria were separated only after their appearance had said they were one.

The ecological species concept groups organisms by the niche they occupy: a species is a set of organisms whose adaptations fit the same particular set of resources and conditions. This is useful exactly where the other two fail, in bacteria and in organisms that reproduce asexually, because a niche can be described whether or not anything interbreeds. Its weakness is that niches are hard to define sharply and often overlap, and that one species can occupy different niches at different stages of its life, which is true of any insect with a larval stage.

In practice biologists apply whichever concept the available evidence allows, and increasingly add a fourth, comparing DNA sequences and drawing the boundary where sequence similarity falls off. In an answer, name the biological concept first, then name whichever alternative applies to the organism in the question.

Morphological species concept

The definition of a species by shared observable structural features, used where interbreeding cannot be tested, as with fossils.

Ecological species concept

The definition of a species by the niche its members occupy, useful for organisms that reproduce asexually.

Viruses and their classification

Every kingdom above is defined by features of cells, and a virus is not a cell and is not made of cells, so viruses are placed in no kingdom. A virus particle is a length of nucleic acid inside a protein coat called a capsid, in some viruses enclosed in an envelope derived from the membrane of the host cell in which the particle was assembled. It has no cytoplasm, no ribosomes, no organelles and no membrane it synthesises itself. It carries out no metabolism, so it does not respire, does not grow and does not respond to anything. It reproduces only inside a living host cell, using that cell's ribosomes, enzymes and nucleotides, which makes it an obligate intracellular parasite. Most definitions of life require several of the things a virus does not do, which is why the usual sentence is that viruses are on the boundary of the living and the non-living rather than that they are alive.

Because the cellular features are unavailable, viruses are classified by the genome. The first division is whether that genome is DNA or RNA, and no virus has both. The second is whether the nucleic acid is double-stranded or single-stranded. That gives four groups, each of which contains known viruses.

Double-stranded DNA viruses include the herpes viruses and the smallpox virus, and they behave most like a cell's own genetic material. Single-stranded DNA viruses are smaller and less common, the parvovirus that causes a serious disease in dogs among them. Double-stranded RNA viruses include rotavirus, the commonest cause of severe diarrhoea in young children worldwide. Single-stranded RNA viruses include influenza, tobacco mosaic virus, the coronaviruses, and the retroviruses such as the human immunodeficiency virus, which carry the enzyme reverse transcriptase and copy their RNA into DNA once inside a host cell.

Two consequences follow. Many RNA viruses have high mutation rates because their polymerases have limited proofreading, which is why influenza needs a new vaccine most years and why an antiviral drug can be defeated within a single course of treatment. Rates differ between groups: coronaviruses encode proofreading activity, so no universal no-proofreading rule holds. And because a virus has no metabolism of its own, it provides no target for an antibiotic: antibiotics act on bacterial ribosomes, cell walls and enzymes, none of which a virus possesses. An antibiotic prescribed for a viral infection has no effect on the virus and selects for resistance in the bacteria the patient is carrying.

Virus

An acellular particle consisting of nucleic acid inside a protein capsid, sometimes with a lipid envelope, which can reproduce only inside a living host cell.

Capsid

The protein coat that encloses the nucleic acid of a virus.