Skip to main content
ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #408800
Research Project: Improved Pest and Disease Control for Enhanced Woody Perennial Tree Crop and Grapevine Production

Location: Crops Pathology and Genetics Research

Title: Full-length ITS amplicon sequencing resolves Phytophthora species in surface waters used for orchard irrigation in California’s San Joaquin Valley

Author
item OTT, NATALIA - University Of California - Cooperative Extension Service
item NOURI, MOHAMAD - University Of California - Cooperative Extension Service
item Browne, Greg

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/7/2024
Publication Date: 8/7/2024
Citation: Ott, N., Nouri, M., Browne, G.T. 2024. Full-length ITS amplicon sequencing resolves Phytophthora species in surface waters used for orchard irrigation in California’s San Joaquin Valley. Plant Disease. https://doi.org/10.1094/PDIS-09-23-1991-RE.
DOI: https://doi.org/10.1094/PDIS-09-23-1991-RE

Interpretive Summary: Diverse Phytophthora species (“water molds”), including many important plant pathogens, have been detected widely among surface water irrigation sources, such as rivers, canals, and reservoirs. In the past decade, metabarcoding (a form of DNA “fingerprinting”) has been used to characterize waterborne Phytophthora populations. In most studies, this involved producing amplicons of either internal transcribed spacer (ITS) region 1 or ITS 2 from Phytophthora spp. (regions of the ribosomal RNA gene commonly used for fungal and water mold diagnostics), followed by indexed high throughput sequencing. However, full- length ITS (1 and 2) sequences are required for resolution of many Phytophthora species. We used metabarcoding with PacBio sequencing of full-length ITS amplicons to analyze populations of Phytophthora in waterways of the Stockton East Water District (SEWD) in the northern San Joaquin Valley of California. The approach yielded species-level resolution of the Phytophthora community at each sampling timepoint and location. Monthly samples were collected during the irrigation season from multiple waterways across the SEWD. Over 30 Phytophthora species were detected in the waterways, including P. cactorum, P citrophthora, P. pini, P. cambivora, P. niederhauserii, and P. mediterranea, which are known pathogens of orchard crops in the area. These pathogenic species were detected throughout the SEWD and during most of the irrigation season. This study demonstrates the utility of full-length ITS amplicon sequencing for identifying Phytophthora species in environmental samples and suggests that some risk may be incurred by orchardists irrigating with SEWD water. Additional epidemiological studies will be required to critically evaluate these risks.

Technical Abstract: Diverse Phytophthora species, including many important plant pathogens, have been detected widely among surface water irrigation sources. In the past decade, metabarcoding has been used to characterize waterborne Phytophthora populations. In most studies, this involved producing amplicons of either internal transcribed spacer (ITS) region 1 or ITS 2 from Phytophthora spp., followed by indexed high throughput sequencing. However, full- length ITS (1 and 2) sequences are required for resolution of many Phytophthora species. We used metabarcoding with PacBio sequencing of full-length ITS amplicons to analyze populations of Phytophthora in waterways of the Stockton East Water District (SEWD) in the northern San Joaquin Valley of California. The approach yielded species-level resolution of the Phytophthora community at each sampling timepoint and location. Monthly samples were collected during the irrigation season from multiple waterways across the SEWD. Over 30 Phytophthora species were detected in the waterways, including P. cactorum, P citrophthora, P. pini, P. cambivora, P. niederhauserii, and P. mediterranea, which are known pathogens of orchard crops in the area. These pathogenic species were detected throughout the SEWD and during most of the irrigation season. This study demonstrates the utility of full-length ITS amplicon sequencing for identifying Phytophthora species in environmental samples and suggests that some risk may be incurred by orchardists irrigating with SEWD water. Additional epidemiological studies will be required to critically evaluate these risks.