Soil harbours a variety of disease causing organisms for both plants and animals. These include microorganisms (fungi, bacteria, actinomyces, phytoplasmas, protozoa and viruses), and larger soil organisms such as nematodes as well as insects (e.g. ants, aphids) and small animals (e.g. slugs, snails, rodents).Plant pathogens may also be spread from plant to plant via insect vectors or by soil animals such as nematodes.

By far the most damage is caused by fungal pathogens which are responsible for a wilts, root rots, club rot & blight. The life cycle for many fungal plant pathogens can be split between above ground on the leaves and shoots (phyllosphere) and below ground in the soil. Many live as saphrophytes, not causing disease, for part of their life cycle whilst others are totally obligate pathogens. Fungal pathogens can be differentiated on the basis of their action on the host; they can either destroy the hosts’ tissue (necrotrophs), such as damping-off caused by Pythium, live as parasites deriving some nutrient/energy from the host (e.g. downy mildew) for possibly long periods or, display properties of both (hemibiotrophs) such as apple scab (Ingram & Robertson, 1999). Toxins may be produced by the pathogen as well as chemicals which regulate the hosts’ metabolism. Bacteria often take advantage of damage such as wounds or natural openings such as stomata to gain entry into the hosts’ tissues. Some diseases cause swellings as a result of their infection to bring about distinct anatomical changes to the plant for example Agrobacterium radiobacter  var. tumefaciens, a bacterial infection of sugar beet causes characteristic swellings to the root tissue brought on by the transfer of DNA from the invading bacterium to the host.

For some plant diseases, soil can be considered a reservoir for the disease organism with the organisms residing in the soil until the right opportunity arises.  However, depending on their life cycle and biology, the time that they can survive in the soil without a suitable host may be limited from a few days to many years. 

Soil conditions play an important part in plant disease affecting the survival of the pathogen, movement through the soil to a potential host or interaction with an antagonist. The amount of water can affect some disease organism more than others. Above ground, very humid conditions tend to promote infection promote downy mildew. Below ground, high levels of water due to poor drainage promote anaerobic conditions which deplete the amount of oxygen available thereby reducing root health leading to greater susceptibility to infection and also to greater movement of pathogen.

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