Detection and quantification of black foot and crown and root rot pathogens in grapevine nursery soils in the Western Cape of South Africa

Black foot disease (BFD) and crown and root rot (CRR) are important soilborne diseases that affect young grapevines in nurseries and vineyards. A 3-year survey (2013-2015) of five open-field grapevine nurseries was conducted in the Western Cape Province of South Africa. The survey involved the isolation of BFD and CRR pathogens from grafted rootstocks (ten plants per nursery, per year) that were rooted in soil for 1 year. In 2013 and 2015, grapevines were sampled, while in 2014, sampling was focused on rotation crops and weeds (ten plants each). The rotation crops included white mustard, lupins, canola, triticale and forage radish. The weed species sampled included Johnson grass, ryegrass, winter grass, Cape marigold and corn spurry. Soil samples from ten sites per nursery were also collected in close proximity to the sampled plants, at depths of 0-30 cm and 30-60 cm (ten samples per depth). Isolations were made from the grapevines, rotation crops and weeds. Pathogen detection and quantification in the soil were determined using quantitative real-time polymerase chain reaction technology. The predominant BFD pathogens isolated from grapevines were Campylocarpon fasciculare, Ca. pseudofasciculare and Dactylonectria macrodidyma. The predominant CRR pathogens were Pythium irregulare and Phytopythium vexans. Dactylonectria macrodidyma, D. novozelandica, D. pauciseptata, Py. irregulare, Py. ultimum var. ultimum and Py. heterothallicum were isolated from triticale roots. Dactylonectria spp. were also isolated from corn spurry, while Py. irregulare and Py. ultimum var. ultimum were isolated from numerous weeds and rotation crops. Mean soil DNA concentrations of Ilyonectria and Dactylonectria were from 0.04 to 37.14 pg mu L-1, and for Py. irregulare were between 0.01 and 3.77 pg mu L-1. The Phytophthora mean soil DNA concentrations ranged from 0.01 to 33.48 pg mu L-1. The qPCR protocols successfully detected and quantified BFD and CRR pathogens in grapevine nursery soil. This is the first report of D. pauciseptata and D. alcacerensis in South African grapevine nurseries.