Download to read offline
Uploaded byForest Research
WP1 Phytophthora distribution, diversity and management in UK nursery systems
This document summarizes the objectives, methods, and progress of a project studying Phytophthora in UK plant nursery systems. The project aims to analyze Phytophthora communities in nurseries using metabarcoding, and model variation among nurseries based on trade, management, and ecology factors. Methods include surveying nurseries, sampling at fine and broad scales, detecting and identifying Phytophthora via sequencing, and providing feedback. To date, over 1000 samples from 15 nurseries have been collected and 395 tested, finding Phytophthora in roots and irrigation water. Next steps include broad-scale sampling, resampling partner nurseries, extracting and sequencing additional samples, and estimating sequencing error rates.
More Related Content
Similar to WP1 Phytophthora distribution, diversity and management in UK nursery systems
WP1 Phytophthora distribution, diversity and management in UK nursery systems
- 1. WP1 ‐ Distribution, diversity and management of Phytophthora in UK plant nursery systems Phyto‐threats project meeting –04 May 2017 David Cooke, Leighton Pritchard, Peter Thorpe, Eva Randall & Beatrix Clark Ana Perez, Sarah Green, Debbie Frederickson Matika ‐ Forest Research Tim Pettit ‐ University of Worcester Bethan Purse ‐ CEH Jane Barbrook ‐ APHA Alexandra Schlenzig ‐ SASA
- 2.
- 3.
- 4. Objectives • WP1 objective I – Using metabarcodingto analyse community structure in nurseries and associated ecosystems – Providing a detailed insight into Phytophthora problems to improve disease management and advise ‘best practice’ • WP1 objective II – Phytophthora community modelling – Seeking explanations for variation in Phytophthora community richness among nurseries – trade, management and ecology
- 5. Methods • Questionnaire – simple (6 questions) to collect basic data on nursery practices •Sampling – Fine‐scale – testing nurseries by project staff for detailed breakdown of management problems and solutions – Broad‐scale – sampling wider nursery selection alongside statutory plant health testing – OPAL – engagement with community sampling • Phytophthora detection and metabarcoding • Computational biology to process large sequence datasets • Interpretation and provision of feedback to owners • Use of data for Community modelling
- 6.
- 7. Sampling – practical issues • Hosts –mix of known and unknown • plant parts – mostly roots • Water flowing through pots – yes but slow • Symptomatic or asymptomatic? both • Control points and contamination hazards (Parke et al 2012 Plant Disease) • Water supply – source and run‐off • Balance between time available and need for detail
- 8. Work programme • Nursery survey –questionnaires and leaflets • Fine‐scale sampling of 10 ‘partner nurseries’ – Critical control points sampled over three years, feedback provided and the effect of mitigations examined • Broad‐scale sampling as part of statutory testing by PMU and APHA – Approx 200 samples from 50 nurseries/garden centres England & Wales and 25 in Scotland to be sampled twice • OPAL project – co‐operation with David Slawson and staff associated with this project – community sampling and engagement in particular areas of recent planting/ regeneration
- 9. Sampling update • 18 sample sets from 15 nurseries (6 English, 1 Welsh, 8 Scottish) • 1009 samples –mostly in triplicate (includes blanks) • 395 PCR tested for Phytophthora to date – Plant roots (93) range of 35 hosts – Water filters (132) – Buffer associated with filter (170) • Washed through plants • Borehole • Ponds/ditches • Equipment washing (e.g. trolleys) • Water blanks
- 10.
- 11.
- 12.
- 13.
- 14.
- 15. Types of nursery • Water – mostly borehole; some mains water (plus rainwater) or river water (‘filtered’) •Plants all above‐ground in cells ‐ to all on or in ground • Production – From holding nurseries/wholesalers importing most stock to entire production of native plants on site • Garden centres/nurseries, trees only, mixed amenity/horticulture and hedgerow trees • Generally good awareness of plant health issues but fungicide use widespread
- 22. Next steps Sampling • Broad‐scale ‐ APHA and PMU –sample instructions and pack drafted for 2017 sampling • OPAL – Co‐ordinating with David Slawson and Vanessa Barber ‐ samples to be collected with communities via contact points in Plymouth, Cardiff, North Wales and Glasgow • Resample fine‐scale nurseries once results known Sample extraction • Extract all root samples • Decision on buffer versus filter extraction
- 23. Next steps Illumina run (May 2017) • Selection of 176 positive findings for first Illumina run • 250 base pair reads, 15M barcode reads = 156K reads per sample •Synthetic control sequences generated to be included in Illumina run as a test of a) sequencing error rate, b) indexing error c) sensitivity range • Pipeline …. Pete Thorpe
- 24.