Collar rot is a symptomatically described disease that is usually caused by any one of various fungal and oomycete plant pathogens. It is present where the pathogen causes a lesion localized at or about the collet between the stem and the root. The lesions develop around the stem eventually forming a "collar". Observationally, collar rot grades into "basal stem rot", and with some pathogens is the first phase of "basal stem rot" often followed by "root rot". Collar rot is most often observed in seedings grown in infected soil. The pathogens that cause collar rot may be species or genera specific. But generalist pathogens such as Athelia rolfsii (aka Sclerotium rolfsii) are known to attack over 200 different species. While bacteria caused collar rot is not common, trees infected with Fire blight (Erwinia amylovora) may develop collar rot. Non-parasitic collar rot may be caused by winter damage.
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The symptomatically described disease Southern blight is often the first observed precursor of the collar rot caused by the fungus Athelia rolfsii. Causally known as Sclerotial blight, Athelia rolfsii survives in the soil as sclerotia, and in infected decomposing plant material as mycelia.
Collar rot that is caused by the oomycete Phytophthora is causally called Phytophthora collar rot, and is a common disease of fruit and nut trees, as well as other flowers and crops. Phytophthora species remain in the soil, as spores, and in infected plant tissue, as mycelia, so absent contol measures (sterilization, toxic applications) the disease continues so long as susceptible plants are grown in that soil.