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. Learn those features and you can place an unfamiliar organism, which a list of example organisms does not let you do.

The scheme is the five-kingdom system of Margulis and Schwartz, a revision of Robert Whittaker's 1969 proposal, and its first division is on cellular organisation. Prokaryotae have no nucleus. Their DNA is circular and lies free in the cytoplasm, with no nuclear envelope around it. They have no membrane-bound organelles of any kind, and their ribosomes are the smaller 70S type. The wall of a bacterium is made of peptidoglycan, a polymer of sugars cross-linked by short peptides that is found nowhere else in nature. That feature is specific in one direction only. Archaea build their walls from other materials, so peptidoglycan identifies a bacterium, not every member of this kingdom.

They are unicellular, usually a few micrometres across, and they divide by binary fission, not by mitosis. They feed in every way there is: absorbing organic material, photosynthesising, and in some cases oxidising inorganic molecules such as ammonium, as the nitrifying bacteria of the nitrogen cycle do.

Describe the drawing

Five cards stacked one under another, one for each kingdom. Each card carries the kingdom name and body plan on the left, whether the cells have a true nucleus and what the cell wall is made of in the middle, and how the organism feeds together with a worked example on the right. Prokaryotae is the only card reading no nucleus, and Animalia the only one reading no cell wall.

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. These are kept out of the plant kingdom because they have no true roots, stems or leaves. More decisively, they do not develop from an embryo kept within the parent plant, as every plant, a moss included, does.

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, 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. They store carbohydrate as glycogen, not 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. Linnaeus worked this way, field guides still do, 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 separate species can look nearly identical; these are cryptic species. 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 where the biological concept fails, in bacteria and in other 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.

Describe the drawing

A six-row grid. Each row names a real case with the facts about it and the answer taxonomists accept: horse and donkey, which breed and give a sterile mule; a male and a female mallard, which look nothing alike; two cryptic Anopheles mosquitoes, identical but not interbreeding; two asexual bacteria; two fossil ammonites; and polar and brown bears, whose hybrids in the wild are fertile. The three columns are the biological, morphological and ecological concepts, and each cell holds the verdict that concept's rule returns for that row, reading one species, two species, or cannot be applied. Cells are coloured by whether the verdict reaches the accepted answer, and no column reaches it in every row.

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. 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 this is 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. So the usual statement is that viruses are on the boundary of the living and the non-living, not 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.

Describe the drawing

A branching diagram starting from the word viruses at the top and splitting into a cyan DNA genome branch on the left and an amber RNA genome branch on the right. Each branch runs down a vertical line and divides again into a double-stranded and a single-stranded form, with named examples printed beneath each: herpes and smallpox, parvoviruses, rotavirus, and influenza, human immunodeficiency virus and tobacco mosaic virus.

Double-stranded DNA viruses include lambda (λ) phage, which infects the bacterium E. coli, 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, Ebola, 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. So influenza needs a new vaccine most years, and an antiviral drug can be defeated within a single course of treatment. Rates differ between groups: coronaviruses encode proofreading activity, so the rule does not hold for every RNA virus. 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.

The same fact decides how an antiviral drug has to work. With no metabolism to poison, the drug must inhibit virus replication inside the host cell, by blocking a step such as entry, copying of the viral genome, assembly of new particles or their release. The safest targets are enzymes the virus codes for itself, such as the reverse transcriptase of HIV, because they differ from anything the host cell relies on, so blocking them does the patient little harm.

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.