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A Desk Study to Review Global Knowledge on Best Practice for Oomycete Root-Rot Detection and Control

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A Desk Study to Review Global Knowledge on Best Practice for Oomycete Root-Rot Detection and Control Project title: A desk study to review global knowledge on best practice for oomycete root-rot detection and control Project number: CP 126 Project leader: Dr Tim Pettitt Report: Final report, March 2015 Previous report: None Key staff: Dr G M McPherson Dr Alison Wakeham Location of project: University of Worcester Stockbridge Technology Centre Industry Representative: Russ Woodcock, Bordon Hill Nurseries Ltd, Bordon Hill, Stratford-upon-Avon, Warwickshire, CV37 9RY Date project commenced: April 2014 Date project completed April 2015 AHDB Horticulture is a Division of the Agriculture and Horticulture Development Board DISCLAIMER While the Agriculture and Horticulture Development Board seeks to ensure that the information contained within this document is accurate at the time of printing, no warranty is given in respect thereof and, to the maximum extent permitted by law the Agriculture and Horticulture Development Board accepts no liability for loss, damage or injury howsoever caused (including that caused by negligence) or suffered directly or indirectly in relation to information and opinions contained in or omitted from this document. ©Agriculture and Horticulture Development Board 2015. No part of this publication may be reproduced in any material form (including by photocopy or storage in any medium by electronic mean) or any copy or adaptation stored, published or distributed (by physical, electronic or other means) without prior permission in writing of the Agriculture and Horticulture Development Board, other than by reproduction in an unmodified form for the sole purpose of use as an information resource when the Agriculture and Horticulture Development Board or AHDB Horticulture is clearly acknowledged as the source, or in accordance with the provisions of the Copyright, Designs and Patents Act 1988. All rights reserved. AHDB Horticulture is a Division of the Agriculture and Horticulture Development Board AUTHENTICATION We declare that this work was done under our supervision according to the procedures described herein and that the report represents a true and accurate record of the results obtained. [Name] [Position] [Organisation] Signature ............................................................ Date ............................................ [Name] [Position] [Organisation] Signature ............................................................ Date ............................................ Report authorised by: [Name] [Position] [Organisation] Signature ............................................................ Date ............................................ [Name] [Position] [Organisation] Signature ............................................................ Date ............................................ AHDB Horticulture is a Division of the Agriculture and Horticulture Development Board CONTENTS INTRODUCTION ................................................................................................................... 1 What are oomycetes? ........................................................................................................ 2 Oomycetes as pathogens .................................................................................................. 3 Life cycles & sporulation .................................................................................................... 5 Oospores: ...................................................................................................................... 7 Asexual spores:.............................................................................................................. 8 Zoospore taxis:............................................................................................................. 12 Dispersal: ..................................................................................................................... 14 Disease ............................................................................................................................ 16 Inoculum: ......................................................................................................................... 40 OOMYCETE DETECTION AND DIAGNOSIS ..................................................................... 46 Background: .................................................................................................................... 46 Molecular Approaches to Disease Diagnosis .................................................................. 47 Immunoassays: ............................................................................................................ 47 Soil case study: ............................................................................................................ 50 New technologies: ........................................................................................................... 51 Nucleoide (mostly DNA-based) assays: ....................................................................... 57 Prospects for uptake of molecular diagnostics in Plant Disease Management Systems (PDMS): ......................................................................................................... 64 TREATING WATER TO CONTROL OOMYCETE DISEASE SPREAD .............................. 67 Deciding whether water treatment is necessary – disease risks associated with water source: ................................................................................................................................ 67 Pasteurisation: ................................................................................................................. 70 Chemical disinfestation of irrigation water: ...................................................................... 73 Ultra-violet irradiation: ...................................................................................................... 83 Biofiltration: ...................................................................................................................... 87 Concluding remarks on water treatments: ....................................................................... 98 OTHER APPROACHES TO CONTROL OF STEM & ROOT ROT OOMYCETES ........... 104 Fungicides: .................................................................................................................... 104 Biological control:........................................................................................................... 108 Cultural control .............................................................................................................. 113 AHDB Horticulture is a Division of the Agriculture and Horticulture Development Board RESEARCH GAPS ........................................................................................................... 117 Diagnostics .................................................................................................................... 117 Inoculum and Disease Risks ......................................................................................... 118 Control Strategies .......................................................................................................... 119 Fungicides, Disinfectants & BCA formulations ............................................................... 121 Costs of water treatment ................................................................................................ 121 REFERENCES .................................................................................................................. 122 WEBSITES ........................................................................................................................ 180 AHDB Horticulture is a Division of the Agriculture and Horticulture Development Board INTRODUCTION With estimates ranging between 500 and 800 species (and counting!), the oomycetes are a large group of fungus-like micro-organisms with representatives in virtually every terrestrial, marine and freshwater habitat worldwide. Many members of the oomycetes are saprophytic, living on decaying plant and animal remains, but a significant proportion of species are also endophytic and/or parasitic, indeed it is claimed that oomycetes are likely all ‘hard wired’ for parasitism (Beakes et al., 2012) with many early divergent genera in their phylogenetic tree being marine parasites of a diverse range of organisms. Some important genera of terrestrial oomycetes are now such specialised pathogens and so strongly co-evolved with their hosts that they have adopted obligate biotrophic lifestyles meaning that they cannot survive and perennate outside living tissues of their specific host species or genera (e.g. the downy mildews and the white rusts). Many other oomycete pathogens are less specialised, being able to attack a wide range of host species, colonising them necrotrophically, whilst a number of Phytophthora species (generally more host-specific species) colonise their host hemibiotrophically –starting off like a biotrophe and colonising still-living host tissues but then progressing to a necrotrophic mode of colonisation – killing and digesting the host’s tissues. There is a vast literature on oomycete plant pathogens both in the UK (including a significant number of AHDB Horticulture-funded studies) and worldwide. A simple Google Scholar search will find between 20 and 80 thousand articles just using simple search terms like ‘Phytophthora’ or ‘oomycete plant pathogens’! Much of this work is focused on key aerial pathogens or pathogen groups
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