Effect of Soil Solarization and Trichoderma Biocontrol Application on Soil Fungal and Prokaryotic Communities Investigated with Next Generation Sequencing.

Soil solarization and application of biocontrol agents have been used to manage soilborne plant pathogens. Treatment effects on soil microbial communities were investigated by Illumina Miseq amplicon sequencing as part of field trials to test soil solarization, alone or with subsequent amendment with the biocontrol agent Trichoderma asperellum (TA), on the survival of two Phytophthora spp. Field trials were conducted during 2012 in San Rafael, CA and in Corvallis, OR. Soil samples from three different depths (5, 15, and 30 cm) were taken before soil solarization, after solarization, and after TA application. The V4 region of the 16S rRNA genes of prokaryotes and the ITS1 region of fungal DNA were sequenced. Communities were clearly separated by site. Soil solarization caused significant changes in both communities, but affected fungal communities more strongly than prokaryotic communities by reducing species richness and diversity. Moisture content was a significant factor affecting the prokaryotic community but not the fungal community. Application of TA did not have a significant effect on microbial communities even though T. asperellum was detected in TA plots. The change in relative abundance of individual taxa as well as taxonomic groups reflects their sensitivity to heat. This study revealed the potential use of the technique to evaluate the susceptibility of each taxon to solarization and biocontrol amendment.