Signs that a plant is diseased

1. Stunted growth is the commonest sign, because a diseased plant diverts resources away from making new tissue or has lost leaf area for photosynthesis.
2. Spots on the leaves mark patches of tissue the plant has killed off and sealed away to stop a fungal or bacterial infection spreading.
3. Areas of decay appear where a pathogen has digested the tissue, leaving it soft, brown and rotting, most often on fruit, stems and roots.
4. Abnormal growths such as galls form when a pathogen makes the plant's own cells divide out of control.
5. Malformed stems and leaves appear twisted, curled or narrowed when a virus disturbs the way new tissue develops.
6. Discolouration ranges from the mottled mosaic of a viral infection to the white powdery coating of a fungus and the general yellowing of leaves that are dying back.
7. Visible pests such as aphids, caterpillars and whitefly are a sign in themselves, since they both damage the plant and carry pathogens between plants.

Diagnosis in the field

1. The first step is careful observation with the naked eye and a hand lens, recording which parts of the plant are affected and how badly.
2. The pattern across a field is as informative as the symptom itself, because an infection usually starts in one patch and spreads outwards over the following weeks.
   1. A problem that appears evenly across the whole crop at once points instead to the soil or the weather, since a pathogen needs time to travel.
3. Whether the oldest or the youngest leaves are affected first narrows the possibilities further, and so does the position of the marks on each leaf.
4. The symptoms are then matched against a gardening manual, an identification key or an online database of photographs of known plant diseases.
5. A hand lens or a portable microscope shows the structures that a photograph cannot, such as fungal threads, masses of spores and the insects feeding on the underside of a leaf.
6. A field testing kit gives a chemical answer on the spot, using a strip carrying antibodies that bind to the pathogen and produce a coloured line within minutes.
   1. Field methods are quick and cheap and need no laboratory, but they can mistake one disease for another that looks similar, so a doubtful result is sent away for testing.

Identification in the laboratory

1. A sample of infected tissue sent to a laboratory can be tested for the pathogen itself, which gives a certain answer rather than a likely one.
2. Antigen testing works because every pathogen carries antigens on its surface whose shape is unique to that species.
   1. Antibodies with a binding site complementary to that antigen are produced, and each one is attached to a coloured dye or to an enzyme that produces a colour.
   2. Ground-up plant tissue is added to a well or a test strip coated with those antibodies, and anything that does not bind is washed away.
   3. A colour appears only if the antigen was present to hold the antibodies in place, so a colour change identifies the pathogen.
3. DNA testing works because the genetic material of each pathogen has a base sequence found in no other organism.
   1. DNA is extracted from the plant sample and copied many times over, so that even a trace of pathogen DNA becomes enough to detect.
   2. Short labelled lengths of single-stranded DNA called probes are added, and each probe has a base sequence complementary to part of the pathogen's DNA.
   3. A probe binds only to the matching sequence, so a signal from the label shows that the pathogen's DNA is in the sample.
4. DNA testing can separate two strains that look identical under a microscope, which matters when only one of them is resistant to the chemical the grower plans to use.
5. A laboratory can also grow the pathogen from the sample on agar and examine its spores at high magnification, which is slower than a test kit but shows the living organism.
6. Laboratory methods are accurate and specific but cost more and take days, so a crop is usually screened in the field and only doubtful cases are sent away.

Ruling out a mineral deficiency

1. An unhealthy plant is not always an infected one, because a shortage of a mineral ion in the soil produces symptoms that look very like disease.
2. A shortage of nitrate ions gives stunted growth and pale older leaves, because nitrate is needed to make the amino acids from which proteins are built.
   1. Without enough protein the plant cannot make new cells, so growth slows and the plant stays small.
3. A shortage of magnesium ions causes chlorosis, in which the leaves turn yellow, because magnesium is a component of chlorophyll.
   1. With less chlorophyll the leaf absorbs less light, the rate of photosynthesis falls and the plant grows poorly even in bright conditions.
4. Three things separate a deficiency from an infection: it affects the whole crop evenly, there are no spots, spores or growths to find under a lens, and it does not spread outwards over time.
5. The diagnosis is confirmed by testing the soil for the ion in question, and by adding a fertiliser containing it and seeing whether new growth comes through green and healthy.