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    Author(s): Ebba Peterson; Joyce Eberhart; Neelam Redekar; Jennifer Parke; Amanda Mills
    Date: 2020
    Source: Proceedings of the seventh sudden oak death science and management symposium: healthy plants in a world with <em>Phytophthora</em>. Gen. Tech. Rep. PSW-GTR-268
    Publication Series: General Technical Report (GTR)
    Station: Pacific Southwest Research Station
    PDF: Download Publication  (355.0 KB)


    Surveys of native wildlands worldwide to determine Phytophthora diversity have found a surprisingly large assortment of root disease-causing species, many of which may contribute to the phenomenon of oak decline. Many species of concern, for example P. cinnamomi, are widely distributed throughout the San Francisco Bay Area. Others, notably P. quercina and P. uliginosa, may additionally contribute to oak decline in Europe (Jung and others 1999, 2002), but are not thought to be widely distributed in the western United States.

    To determine Phytophthora diversity and distribution in the Midpeninsula Regional Open Space District (MROSD), we collected soil from 30 planted restoration sites, 12 planned restoration sites and 29 adjacent, minimally disturbed non-planted areas in December 2017 and 2018. In addition to baiting, we extracted DNA from a 10 g subsample of each soil. The ITS1 region was amplified and PCR products were submitted for Illumina MiSeq high-throughput sequencing. During the 2018 sampling, we additionally returned and re-sampled sites with strong DNA-only detections of the P. quercina-cluster (which may be P. quercina and/or P. versiformis) and the P. uliginosa-cluster (which may be either P. uliginosa and/or P. europaea) in an attempt to bait these species from soils.

    Phytophthora was detected at all 9 MROSD preserves sampled. The P. quercina-cluster and the P. uliginosa-cluster were widespread, being detected via Illumina MiSeq in either 6 or 5 preserves, respectively. Nearly all detections were from non-planted areas, found in association with overstory oak or tanoak.

    We were unable to obtain any isolates matching P. quercina or closely related species. To confirm the identity of P. quercina in the DNA extracts, we additionally sequenced these extracts with the MinION sequencer, which provides longer (1,000 bp) read lengths. This revealed this OTU was an approximate 90% match to the P. quercina-cluster and likely represents a taxon not present in our database. In 2018, we recovered three isolates from two preserves with ITS1 sequences poorly matching to P. europaea. Subsequent sequencing of the COX region revealed these isolates are P. sp. ‘cadmea’ which was only recently recovered by Bourret (2018) in a neighboring county. This new taxon has not been evaluated for its risk to native flora.

    Illumina MiSeq high-throughput sequencing is a useful tool to study the distribution of hard to bait taxa; however, DNA-only detections are difficult to interpret without isolates to confirm their identity, viability, and pathogenicity.

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    Peterson, Ebba; Eberhart, Joyce; Redekar, Neelam; Parke, Jennifer; Mills, Amanda. 2020. Distribution of Phytophthora quercina and other oak-root Phytophthora pathogens in the Midpeninsula Regional Open Space District. In: Frankel, Susan J.; Alexander, Janice M., tech. cords. Proceedings of the seventh sudden oak death science and management symposium: healthy plants in a world with Phytophthora. Gen. Tech. Rep. PSW-GTR-268. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 96-97.

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