Sample volume affects the number of Phytophthora and Phytopythium species detected by soil baiting

Phytophthora species are detected from environmental samples through DNA metabar-coding than are isolated by baiting. We investigated whether bulking soil samples and baiting similar to 300 g samples in standard 1 L tubs resulted in the isolation of fewer Phytophthora and Phytophythium species compared with using 15 - 20 g samples of non-bulked soil in individual 200 ml tubs. At each of four sites with dying vegetation, 50 soil samples were collected and baited separately in small tubs, followed by plating of lesioned baits over 7 days. The number of Phytophthora species obtained was compared with those obtained from bulking the 50 samples and baiting subsamples in large tubs. Half of the asymptomatic baits were plated on day 7 and the remaining were assessed for the presence of Phytophthora using metabarcoding. Root samples with rhizosphere soil from the bulked soil in each site were also assessed using metabarcoding. A higher number of Phytophthora species was recovered from each site from baiting small volumes of non-bulked soil than large volumes of bulked soils. Metabarcoding of the asymptomatic baits revealed species not isolated from lesioned baits. More species were detected from the roots using metabarcoding than were isolated from baits. Metabarcoding did not reveal any species from the rhizosphere soil and roots that were not also detected from metabarcoding of the asymptomatic baits and/or plating. The numbers of Phytopythium species detected using the different methods followed the same trend as for Phytophthora. It was concluded that baiting small samples from across a site in separate small tubs results in the isolation of a higher number of Phytophthora species than the standard technique of baiting large samples of bulked soils, and that this, together with metabarcoding of asymptomatic baits, detects the highest total number of species.

Automated summary

More Phytophthora species can be detected from environmental samples using DNA metabarcoding compared to isolation by baiting. Baiting small volumes of non-bulked soil samples resulted in the recovery of more Phytophthora species than baiting large volumes of bulked soils. Metabarcoding of asymptomatic baits detected additional species that were not isolated from lesioned baits. The combination of baiting small samples and metabarcoding of asymptomatic baits yielded the highest number of total species detected.