Lack of essential minerals (nitrates/magnesium ions)
nitrates are proteins that plants need for growth, so plants without nitrates have stunted growth.
magnesium ions are needed for making chlorophyll, which is needed for photosynthesis. plants with a magnesium deficiency often suffer chlorosis (yellow leaves).
Other common symptoms:
Abnormal growths/lumps
Malformed stems/leaves
Patches of decay
Spots of discolouration on their leaves
Or you might be able to see the organism responsible like aphids or spider mites
Diagnosing disease
Take basic observations and try to match what you see to the disease listed online or in a manual
Send a sample to a plant pathologist who can do more detailed testing (take tissue sample in and use a microscope to see in more detail, or look for particular antigens and pathogens)
Plant pathologist run DNA test
Trial and Error
If plant has yellow leaves, it may have a magnesium deficiency, so attempt to give it magnesium. See if it works. If it doesn't try something else.
Plant defences
Physical- physically prevent the entry of pathogens such as cellulose cell walls, waxy cuticle, layer of cells around stems (bark)
Chemical- chemicals the plants can secrete such as antimicrobial chemicals and poisons
Mechanical- more of a function than just a barrier such as thorns and hairs to stop animals eating and touching or leaves that curl or drop if insects land on them