The soil-borne oomycete pathogen Pythium (several species) can attack roots and crown tissue. Young plants are more susceptible due to tender stem tissue. Wet soils provide favorable conditions for the pathogen to develop. Cool soils are also favorable, but moisture is most important. Thus crown and root rot is more likely to develop in spring. It has been observed occasionally on Long Island. Plants in the photographs below were observed on 3 June 2015. More commonly a related pathogen, Phytophthora capsici, is found affecting pepper. Symptoms caused by Pythium are brown, sometimes shriveled tissue at the base of the plant extending up almost 1 inch. Internal tissue is also brown. With Phytophthora blight this tissue is dark brown to almost black, and often extends further up the stem. The outer part of the ends of roots rot off leaving the white core; this is characteristic for Pythium. The tops of plants become dead and brown as a result of the damage to crown and root.
Avoiding wet soil conditions is important for managing the soil-borne oomycete pathogens. Thus it is important not to over irrigate especially when plants are small. Infection can occur when soil is saturated for as little as 5 to 6 hours. This disease is more likely to occur where soil is compacted or water drains slowly into soil for another reason. These pathogens can move in the film of water on the underside of plastic, thus it can be helpful to cut plastic mulch making a break between diseased and healthy plants, especially where affected plants are occurring in groups. Pulling these plants and discarding outside the field will reduce the amount of pathogen present. Disease is more likely to occur in peppers grown with black plastic mulch.
Pythium can survive in soil for long periods primarily because they produce a spore (oospore) that can survive in soil for years. Thus the disease is challenging to manage through crop rotation. Rotation is recommended used routinely beginning before crown and root rot is a problem.
Incorporating a lot of plant tissue, such as over-wintered cover crop, into soil just before planting can provide favorable conditions for Pythium.
For commercial growers there are several biopesticides that can be applied to soil before transplanting or in transplant water as well as afterwards, including Actinovate, Bio-tam, Double Nickel, Regalia, Serenade Soil, and Soilgard. These are approved for organic production. The chemical fungicide Previcur Flex can be applied by directed nozzles to the lower portions of the plants and surrounding soil, or via drip irrigation, transplant/ setting water, or as foliar spray or by sprinklers (foliar applications are best with bare-ground plantings and followed by irrigation to move the fungicide to the soil). Previcur Flex is not effective for Phytophthora capsici, thus accurate diagnosis is important. It is important to apply these products such that they get to crown and root tissue, and to use a preventive program.