Modeling Survival of Soilborne Phytophthora spp. and Characterizing Microbial Communities in Response to Soil Solarization and Biocontrol Amendment in Container Nursery Beds

Graduation date: 2015In horticultural nurseries for container-grown plants, production and sales have been threatened by the presence of a quarantined plant pathogen, Phytophthora ramorum (causal agent of sudden oak death). Infested nursery beds are an important source of P. ramorum, which can initiate disease through movement with surface water to infect roots or can be splashed onto foliage. My research objectives were 1) to investigate the potential use of soil solarization (solar heating of soil) to control soilborne P. ramorum and another species Phytophthora pini, 2) to examine solarization effects on an introduced biocontrol agent Trichoderma asperellum and on indigenous soil microbial communities, and 3) to determine the major factors defining survival of the pathogens and to develop a useful mathematical model to predict the minimum time period required for solarization to kill the pathogens. Field trials were conducted in San Rafael, California (CA) and Corvallis, Oregon (OR) U.S.A. with rhododendron leaf disk inoculum infested by P. ramorum or P. pini. In lab experiments, thermal inactivation curves were determined for inoculum of both species exposed to stable high temperatures. P. pini had greater heat tolerance than P. ramorum. Both species survived high temperature treatment longer at lower water potentials than at higher water potentials as demonstrated in polyethylene glycol solutions as well as in soil. Intermittent heat was less effective in killing the pathogens than was continuous heat for the equivalent total heat exposure period. The rate of physiological damage to the inoculum was not constant but rather increased with exposure to continuous heat. In contrast, damage from multiple sub-lethal heat events accumulated at a constant rate, allowing calculation of total damage as the sum damage from each heat event. A predictive model was established with the parameters of temperature, water potential, and intermittent heat regime effects based on lab experiments. The model was tested with inoculum recovery data from field trials in bare soil, or soil covered with a 5- or 7.5-cm- thick layer of gravel as is typical of container nurseries. The presence of a gravel layer in solarized plots increased belowground temperature relative to plots without gravel and resulted in a lower water potential of leaf disk inoculum placed at the surface or buried within the gravel layer. The prediction of inoculum survival time was significantly improved by adding the factors water potential and intermittent heat regime to the model in addition to temperature. Solarization enhanced subsequent establishment of T. asperellum although there was no significant reduction in Phytophthora spp. recovery after application of the biocontrol agent. High throughput sequencing analysis with the Illumina Miseq platform revealed the response of soil prokaryotic and fungal communities to solarization and demonstrated heat sensitivities of individual taxa. This study resulted in development of a mathematical model to predict critical conditions of temperature and moisture necessary to kill soilborne inoculum of Phytophthora spp. during soil solarization, and contributed to an understanding of solarization effects on an introduced biocontrol agent and on indigenous microbial communities