The single term used to describe underground, soil line, or crown rots of seedlings due to unknown causes is damping-off . The term actually covers several soil borne diseases of plants and seed borne fungi.
Rhizoctonia root rot (Rhizoctonia solani) is a fungal disease which causes damping-off of seedlings and foot rot of cuttings. Infection occurs in warm to hot temperatures and moderate moisture levels. The fungi is found in all natural soils and can survive indefinitely. Infected plants often have slightly sunken lesions on the stem at or below the soil line. Transfer of the fungi to the germination room or greenhouse is easily accomplished by using outdoor gardening tools inside or vice versa. The germination room should not be used for mixing potting soils or transplanting seedlings as a general rule.
Pythium Root Rot (Pythium spp.) is similar to Rhizoctonia in that it causes damping-off of seedlings and foot rot of cuttings. However, infection occurs in cool, wet, poorly-drained soils, and by overwatering. Infection results in wet odorless rots. When severe, the lower portion of the stem can become slimy and black. Usually, the soft to slimy rotted outer portion of the root can be easily separated from the inner core. Species of Pythium can survive for several years in soil and plant refuse.
Phytophthora root rot (Phytophthora spp.) are usually associated with root rots of established plants but are also involved in damping-off. These species enter the root tips and cause a water-soaked brown to black rot similar to Pythium. These fungi survive indefinitely in soil and plant debris.
Black root rot (Thielaviopsis basicola) is a problem of established plants. It does not occur in strongly acid soils with a pH of 4.5 to 5.5. It usually infects the lateral roots where they just emerge from the taproot. The diseased area turns dark brown, and is quite dry. The fungi survive for 10 years or more in soil.
Miscellaneous fungi causing similar symptoms include Sclerotinia (white mold), Sclerotium rolfsii, Macrophomina phaseoli, some species of Botrytis (gray mold), Aphonomyces, Fusarium, Cylindrocladium, and others. Hence the need for the collective term known as damping-off.
Seeds may be infected as soon as moisture penetrates the seed coat or a bit later as the radicle begins to extend, all of which rot immediately under the soil surface (pre-emergence damping-off). This condition results in a poor, uneven stand of seedlings, often confused with low seed viability. Cotyledons may break the soil surface only to whither and die or healthy looking seedlings may suddenly fall over (post-emergence damping-off). Infection results in lesions at or below the soil line. The seedling will discolor or wilt suddenly, or simply collapse and die. Weak seedlings are especially susceptible to attack by one or more fungi when growing conditions are only slightly unfavorable. Damping-off is easily confused with plant injury caused by insect feeding, excessive fertilization, high levels of soluble salts, excessive heat or cold, excessive or insufficient soil moisture, or chemical toxicity in air or soil.
Above ground symptoms of root rot include stunting, low vigor, or wilting on a warm day. Foliage of such plants may yellow and fall prematurely starting with the oldest leaves. The roots of a diseased plant will have some shade of brown or black and evidence of water-soaking. Healthy roots are fibrous appearing and are usually white or tan in color. These symptoms are easily confused with severe mite, aphid, scale infestations, or root-feeding by nematodes or insect larvae. Environmental factors such as accumulated salts in the soil, insufficient light or nitrogen, potbound roots, cold drafts, etc. can be eliminated only by examination of the roots.
Fungicides may be applied as a soil drench after planting. They may be incorporated into the soil before planting as a dust. They can be sprayed in mist form on all seedlings as a precaution until they have been transplanted into individual pots. Once transplanted, only those seedlings known to be especially sensitive to damping-off need be misted with fungicide daily until the first or second seed leaves have emerged. The following chemicals are not recommended for use by the average recreational gardener, but may still be available for use (if not yet banned), providing the manufacturer's instructions are followed to the letter.
Captan (sold as Captan) controls most pathogens, but not Rhizoctonia.
Metalaxyl (sold as Subdue or Apron) controls Pythium, Phytophthora, and Aphanomyces.
Iprodione (sold as Chipco) controls most pathogens, but not Pythium, Phytophthora, or Aphanomyces.
Etridiazole and Thiophanate-methyl (sold as Banrot) controls most all pathogens.
PCNB-etridiazole (sold as SA-Terraclor or Super-X) good general purpose fungicide.
PCNB-quintozene (sold as Terraclor, Fungi-clor, or PCNB) controls Rhizoctonia and Sclerotinia species.
Fosetyl-A1 (sold as Aliette) controls Pythium, Phytophthora, & Aphanomyces.
Well, you get the idea. There are too many to list, and they go on and off the market very quickly (mostly because they are very dangerous when used improperly, and some are too dangerous to have been put on the market at all.)
Biocontrol with microbial fungicides is being investigated in several academic labs. Typical targets are those plants being mass-produced in nearby commercial greenhouses. Early results indicate damping-off prevention comparable to that achieved with the use of standard fungicidal drenches like those mentioned above. However, there remain some notable drawbacks in biocontrol of damping-off.
First, microbial fungicides act against only one species of root or stem rot, and must be applied in advance. So, in order to prevent damping-off, you must know in advance which species of Pythium or Rhizoctonia or other fungi is likely to attack your crop. That limits their use to large production facilities.
Second, some formulations of microbial fungicides have been shown to produce substances that are phytotoxic to certain crops.
Finally, small changes in environmental conditions during test periods seem to cause significant differences in test results.
There is much work to be done in this area of biocontrol, not to mention the ultimate necessity of EPA approval. Use of biocontrol agents for prevention of damping off by home gardeners may well be decades away. For a list of those biocontrol products which have approval for controlling plant diseases, go to the USDA ARS Biocontrol Plant Diseases Laboratory at http://www.barc.usda.gov/psi/bpdl/bpdl.html