Current state of knowledge and research needs for managing oomycete root diseases: outcomes of the workshop held by HDC on 1 st October 2012

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1 Current state of knowledge and research needs for managing oomycete root diseases: outcomes of the workshop held by HDC on 1 st October 2012 Contents Page Background 2 Presenting the current state of knowledge 2 An overview on the detection, identification & control of oomycete pathogens 2 Dr Martin McPherson (Stockbridge Technology Centre Ltd.) Campaign tactics: know your enemy 3 Dr Erika Wedgwood (ADAS Boxworth) Biological Control: Disease management in organic brassica seed and transplants 4 Dr John Clarkson (Warwick Crop Centre) Dr Steve Roberts (Plant Health Solutions Ltd) Oomycete diseases in fruit crops with special reference to crown rot of Strawberry 5 Dr Robert Saville (East Malling Research) Oomycete control: Theory into practice - or - application of experimentation into practice 6 Dr Tim Pettitt (Eden Project Ltd.) Summaries of discussions 8 Conclusions 10 Appendix 11 1

2 Background Oomycete root diseases, caused mostly by species of Phytophthora and Pythium, present problems which impact across the majority of horticultural production systems in the UK. Since the HDC was formed in 1986, it has funded more than forty projects to find ways to limit their impact (see Appendix 1), but in spite of this highly targeted work progress has been slow. Up to now, our approach has mostly been to develop projects to deliver solutions to highly specific problems faced in individual crops or at most, panel sectors. Whilst this tactical method is highly responsive to industry needs, it can be inefficient because of the large administrative cost involved in managing large numbers of small contracts, and also misses the potential to pool resources for more challenging projects which require greater investment but which have a better chance of delivering better solutions. Presenting the current state of knowledge An Oomycetes root diseases workshop was held at Stoneleigh 1 st October 2012 with the objective of bringing together the leading researchers and practitioners in the field of oomycete root disease management to present the existing state of knowledge and their understanding of knowledge gaps that need to be filled to representatives from across all relevant sectors of the horticultural industry and to facilitate a discussion to determine the direction of future research. Presentations (PDF files available from HDC website): An overview on the detection, identification & control of oomycete pathogens Dr Martin McPherson (Stockbridge Technology Centre Ltd.) Dr McPherson presented a comprehensive overview of oomycetes, detailing their evolutionary background and why they are so different in behaviour and response to control methods from the genetically distinct conventional fungi. His presentation included a wealth of diagrams, photographs and video footage of oomycete diseases and zoospores in action. Information on detection techniques was also provided; experienced pathologists can go a long way through recognising symptoms and by knowing which species are susceptible to which pathogens, i.e. what gets what! Beyond this, techniques such as direct microscopic examination are used, incubating infected plant material at high relative humidity, aqueous cultures, baiting techniques and for facultative species, isolation to artificial agar media. Diagnostics technologies such as ELISA and LFD (lateral flow devices) are becoming available, and increasingly, molecular diagnostics. Accuracy of pathogen identification is usually important to genus level, but species level may not be needed since this step is difficult and expensive, particularly bearing in mind that control measures will usually be similar. Serology and molecular techniques are improving, but not sufficiently refined yet for identifying all species in the key genera Pythium, Phytophthora & Aphanomyces. At present, pathogenicity testing is usually the most relevant decisionmaking process for effective control. Dr McPherson emphasised the crucial role of water in oomycete pathogenicity they are also called water moulds because they are unable to complete their lifecycles without free water. They therefore naturally prefer wet conditions classically seen in both potato blight and downy mildew. Their highly motile zoospores enable very rapid dispersal in water, and therefore Pythium and Phytophthora are very much at home in hydroponic systems. Furthermore, water collection for reuse needs very careful thought knowledge of control systems is essential and monitoring of water quality of continuing importance. Active disinfection systems currently deployed include pasteurisation, ultra violet light, 2

3 copper, chlorine dioxide, ozone and microfiltration, whilst an effective passive system is available through slow sand filtration. Hydroponics technologies also need to be considered carefully hygiene in ebb and flood systems, for example, is crucial as a single infected plant can spread zoospores very rapidly around an entire irrigation system. Slow sand filtration is an established technology which has been shown to be highly effective against Pythium and Phytophthora but which has yet to be fully exploited by UK horticulture probably because of a lack of understanding within the industry. For effective disease management, growers need at least a basic knowledge of the biology and epidemiology of the pathogens they are seeking to control as many factors impact on the risk to their crop. The first objective is exclusion zoospores are the most vulnerable stage of the lifecycle and can be killed, for example, by the use of a wetting agent in irrigation water. Oospores are long-lived and are the most difficult to eradicate where possible the emphasis must be on removing infected plant material. Disinfectants can minimise disease carryover, e.g. on trays, and soil sterilisation is possible although the loss of methyl bromide limits options. Chemical controls remain as the main opportunity for managing oomycete diseases, but because this group of pathogens evolve so rapidly, resistance is a major threat to the efficacy of the grower s armoury. The HDC is addressing this problem by screening new candidate products through the SCEPTRE programme and ongoing EAMU registrations. Ultimately, however, the future security of this approach is dependent on at least one oomycete pathogen causing serious economic damage in a major agricultural crop (currently Phytophthora infestans on potatoes and Plasmopara viticola on grapes), thereby providing a large enough market to justify development and registration costs. Campaign tactics: know your enemy Dr Erika Wedgwood (ADAS Boxworth) Dr Wedgewood s presentation looked at understanding a pathogen group which attack our crops across the globe, asking these key questions: Can we grow crops that can fight back? What can we do to kill or repel these enemies? Understanding pathogens necessitates identification since without this we won t know which ones cause problems. Molecular methods have confirmed 120 species of Phytophthora to date, knowledge facilitated by research funding followed devastating losses to P. ramorum & P. cinnamomi. Information regarding Pythium is poorer we have an incomplete molecular reference base for identification and are lacking for morphological identification & pathogenicity tests. We don t necessarily know which species are currently damaging or are a potential threat; alien plants can bring pathogens into the UK which were apparently innocuous in their native state but then turn nasty in the new conditions, e.g. Phytophthora infestans and P. kernoviae. Unfortunately import regulations require pathogen species to be specified before any restrictions on host plant entry to the UK can be implemented, despite this knowledge. And the picture is often far from simple e.g. HNS 181: Survey detection and diagnosis of Phytophthora root rot and other causes of die-back in conifers found a huge complex of species in root-rotted conifers with seven Phytophthora species and seven Pythium species identified, and to add to the confusion, pathogenicity differs between hosts. More understanding of what confers host plant resistance is needed why are some conifers & raspberry cultivars more susceptible to Phytophthora root rot & some carrot varieties to Pythium cavity 3

4 spot is resistance obtained through physical structure of roots, chemical exudates and/or microbial flora? Research has shown that plant secondary metabolites such as tannins stop oomycete development in laboratory conditions, whilst zoospores are seen to swim to root exudates of susceptible hosts. Microorganisms also have a part to play in oomycete management - microbial supplements/feeds e.g. Revive (Bacillus subtilis), Trianum (Trichoderma sp.) compost tea, and mycorrhizal products may outcompete pathogens and/or elicit production of defensive chemical by the potential host plant. Biofungicides also have enzyme/biostatic effects e.g. Prestop (Gliocladium sp., Serenade ASO (B. subtilis strain), T34 (Trichoderma sp.). More research on species composition in soils & nutrient solutions will give us a much greater understanding of what is happening in, for example, replant sickness & microbial supplement/stimulant use. Water bodies are an important place to focus control activities - not all reservoirs can be covered or protected from runoff so we need ways of removing pathogens. Possibilities include ultrasound resonance, where preliminary tests have shown mycelium and zoospore disruption. Another possibility is using leaves, fruit and seeds as bait to attract and collect zoospores having been trapped, spores can then be killed. Filtration is also a potential solution, using geotextiles or other media to physically remove zoospores from the environment to be protected. Other options include the use of chemicals to trigger zoospore release from cysts/roots which are then much more vulnerable to control measures. Chemical controls: potassium phosphite injections have been shown to be effective in trees against Phytophthora in Australia and the USA for up to five years. The ornamentals sector will benefit from trials with a view to obtaining EAMUs for, e.g. new potato fungicides as substitutes for metalaxyl. New trials are also needed for disinfectants as currently available information needs updating, and alternatives to banned soil fumigants are needed. Potential research to learn more about the pathogens and ways to overcome them: What suppresses surprise UK pathogens in their native habitat? Quantitative PCR for species/thresholds in soil Microbial treatments in growing media/soil Why are some plants more resistant / what makes some oomycetes spp. more pathogenic? Trapping/ultrasound zoospores in water Chemical disinfectants & fungicides including those derived from natural products Biological Control: Disease management in organic brassica seed and transplants Dr John Clarkson (Warwick Crop Centre) Dr Steve Roberts (Plant Health Solutions Ltd) Drs Clarkson and Roberts reported findings from a recent research project funded by HDC; FV Disease management in organic brassica seed and transplants. The objectives of this work were to evaluate organically acceptable brassica seed and transplant treatments for controlling Pythium- and Rhizoctonia-induced damping off and the seed borne pathogens Phoma and Alternaria. In the search for oomycete control options, the biological control agents (BCAs) Trianum (Trichoderma harzianum T22), Prestop (Gliocladium catenulatum), Mycostop (Streptomyces griseoviridis), Subtilex (Bacillus subtilis), Revive P (Bacillus subtilis), Trichoderma viride S17A (Warwick) together with composted green waste (CGW) + Trianum and CGW +T. viride S17A were tested for efficacy against Pythium in comparison to a fungicide-treated (thiram) control. 4

5 In summary, the results were: BCAs were ineffective against Pythium damping-off when applied at sowing. Prestop and Endofine (and Trianum G in one experiment) significantly reduced Pythium if added to the growing medium two weeks before sowing. Green waste compost treatments significantly reduced damping off caused by Pythium with or without BCAs added. BCAs can be inconsistent and often this is associated with pathogen inoculum levels / disease pressure. Getting watering right has the biggest impact of all Issues for development arising from this work are: How do we get BCAs to work? Which are the most appropriate products and when do we apply them? If it doesn t work why not? Which are the important environmental factors, including substrate, temperature and moisture Which formulation seed treatments or granule application? Which Pythium or other oomycete species are important? At present we know of 250 Pythium species; many are soil inhabitants and are saprophytic; some show promise as BCAs. The main species causing damping-off is probably P. ultimum but others may be more important depending on crop e.g. P. aphanidermatum. What is prevalence of Phytophthora which can also cause damping off symptoms? Oomycete diseases in fruit crops with special reference to crown rot of Strawberry Dr Robert Saville (East Malling Research) Dr Saville s presentation began by outlining issues in top fruit production: Soilborne Phytophthora spp. cause diseases of the root and crown (sometimes called collar rot) affecting apples and cherries, although pears and plums are largely resistant. Perhaps predictably for free water-dependent pathogens, diseased trees are commonly found in poorly drained areas of the orchard. Visible symptoms include reduced tree vigour, leaf chlorosis and eventual collapse or death of the tree. A diagnostic reddish-brown lesion forms on the inner bark and wood. A sharp line demarcates the reddish-brown (diseased) and white (healthy) portion of the crown. In soft fruit, Raspberry root rot, caused by Phytophthora fragariae var. rubi results in reduced vigour (lack of new growth is noticeable in the spring), wilting, early autumn leaf colours and premature leaf drop, black/brown lesions at the base of canes, dead and dying roots. Strawberry red core/stele caused by Phytophthora fragariae. Stunted plants, leaves exhibiting a blue/green appearance leading to plant collapse and death resulting from root death. Roots exhibit characteristic red colour in cortex of root. Strawberry crown rot, caused by Phytophthora cactorum, can result in significant losses in fruit production- typically the youngest leaves turn blue-green and wilt, then depending on the number of crowns affected, all or part of plant wilts and dies. Affected plants that survive may be stunted. Protected crops are more vulnerable and susceptible varieties can lose entire crops. Major losses can 5

6 also occur in plant propagation, particularly in module plants the presence of crown rot can lead to rejection of the whole stock. The disease has been on the increase in the UK since 1989 due to increased cultivation of susceptible varieties, e.g. Elsanta. Recent HDC-funded research - SF121 Evaluation of products for control of crown rot in strawberry - has validated a range of chemical treatments, and HDC is taking the work forward within SCEPTRE. Looking forward, effective control programmes need to be fully integrated to make best use of all tools available to the grower, including cultural control, protectant fungicides, disease-free planting material, genetic resistance, understanding key issues such as route of introduction, symptomless infection and epidemiology, all aided by sensitive diagnostic tests. Oomycete control: Theory into practice - or - application of experimentation into practice Dr Tim Pettitt (Eden Project Ltd.) Dr Pettitt s presentation began by outlining his experience in managing Pythium root rot in all-yearround chrysanthemums, where a simple pathogenicity test distinguished pathogenic colony-forming units (CFU) and established that disease prevalence was directly related to pathogenic CFU numbers. Practices that caused spikes in pathogenic CFU numbers could then be identified and avoided. Phytophthora root rot in HNS: large amounts of Phytophthora inoculum are produced in short periods and spread quickly symptoms are often not immediately visible, but their presence can be detected by using a series of technologies including enzyme-linked immunoassay (ELISA), zoospore trapping immunoassay (ZTI), plating, baits and dipsticks. Testing water for oomycete presence is vitally important even sparklingly clear water samples can be shown to harbour large numbers of pathogenic Pythium CFUs per litre. Different categories of water tests are available to growers: 1 Water treatment efficacy testing unspecific; can be highly sensitive but identifications of only medium importance 2 Problem specific - e.g. looking for Phytophthora ramorum 3 Health checks a) are my storage and irrigation lines clean? same as 1. b) Checks on collection ponds, open reservoirs etc. should I do anything to this water before using it? - (almost undoubtedly yes!) trickiest of all as high sensitivity rapid identifications needed How can these tests be improved? 1. Water treatment efficacy tests: How do we increase sensitivity? Baits, plating, other approaches? Also sampling strategies is 1 litre sufficient? Mechanical samplers? 2. Problem-specific: Molecular diagnostics improving all the time and probably in the longerterm extremely sensitive broad screens with specific identifications will become available 3. Health checks : this leads to general biology, epidemiology and interactions between the various oomycetes and other organisms in water/nutrient solutions 4. Designing testing regimes: better understanding of questions to ask and of benefits and upfront costs should we aim for increased/improved in situ tests? 6

7 Water Treatment We know that a wide range of water treatment technologies work very well in the control of oomycete diseases Selection of appropriate technologies = very much horses for courses Sustainability of treatment technologies needs to be better explored some look very promising but have not been fully evaluated Promising approaches such as chlorine dioxide use have not been properly assessed in context Interesting approaches like the iris bed system apparently work but exactly how and what the limits of efficacy are is unknown. Iris beds Pythium propagules definitely enter them but rapidly decline in numbers and have not been detected exiting them - is this luck? Non-pathogenic oomycetes of genus Saprolegnia live quite happily throughout these systems. If there is selective exclusion, how does it work? And what are its limits? 7

8 Summaries of discussions Breakout groups representing Vegetables, Protected Ornamentals, Fruit and Hardy Nursery Stock followed up the presentations by discussing which issues most affect their sectors and what they would like to see resolved. Vegetables: Queries/requests: Need to know more about virulence and host ranges, particularly what triggers expression of symptoms in plants previously infected but not showing signs of damage (i.e. silent infection)? Effective control needs to be at or before planting ideally in seed treatments (or by using genetic resistance). Why is damping off almost always localised and only ever significant in young plants? Can seedling vigour be improved to get beyond vulnerable stage as soon as possible? What is the natural suppressiveness of different growing media and combinations? Whole system approach needed for biological control agents - need to know how to optimise their contribution rather than expect silver bullets. Is it possible to make green waste safe, both microbiologically and avoiding herbicide carryover? Can we trigger/lure zoospores to non-host or break dormancy in oospores? What are the practical issues for managing pathogens in collecting, storing, reusing and which are the best ways to disinfect water? What sampling and monitoring regimes are necessary to maintain safe practice? Workshop needed and HDC knowledge transfer opportunities here Can the same technologies used to control algae (e.g. copper, ultrasonics) work on oomycetes? Chlorine dioxide rates of application need optimising Need curative fungicides Protected Ornamentals: Main impacts on plants: root death; substrate suppression helping in PO sector Location of problems and timings Ebb and flood will be biggest issue but not typical for PO sector Importing problems with young plants (and also seed) included Danish trolleys Symptom expression spring and autumn but there year-round Costs: Can be huge - 40m Impatiens on downy mildew has cost producers 40m annually at farm gate prices; one case of Phytophthora in pansies resulted in 50% crop loss. Losses often undiagnosed and are likely to be higher cost than growers realise Monitoring/diagnostics Growers need to use monitoring and diagnostics Testing of substrates need guidance on practicalities, e.g. 200 samples/year/site? Need to move towards pre-emptive approach and away from fire fighting what costs are likely? Control Considered to be relatively well-covered by chemical control options 8

9 Fruit Impacts: oomycetes cause major losses in most fruit crops through killing plants Location and timing of problems Strawberry: crown and roots Propagation to fruiting Raspberry: roots Propagation to fruiting Apple: crown, roots & fruit During season in orchard; 3-4 weeks before harvest and into storage Costs: Strawberries m, Raspberries m, Apples 100k Monitoring/Diagnosis Plant health inspection inexact diagnostics required Forecasting Every year, but variable year-to-year dependent on weather Current controls Over-reliant on a few materials, e.g. Paraat every 2 weeks in NL; resistance is certain Environmental management Favourable microclimate useful to reduce impact of infection Water quality Key area, across all sectors Acceptable price to grower WHATEVER IT TAKES Hardy Nursery Stock Main issues: Replant in Rosaceous crops Phytophthora cambivora in river water Stem Phytophthora Key crops affected: Rhamnus (Ph) Aucuba (Ph,Py) Cytisus (Py) Euphorbia (Ph) crash after potting Chaemacyparis (Ph) Pinus (Py) Choisya (Ph) aerial/upper stem Heathers (Ph,Py) Taxus (Ph) Rhododendron (Ph) aerial/upper stem Hydrangea paniculata (Ph,Py) Alder (Ph) Ceanothus (Ph) aerial/upper stem Geraniums (Ph) Daphne (?) Fremontodendron (?) aerial/upper stem Penstemon (Ph) Pieris (Ph) Garrya (Ph,Py) Ribes (Ph) Convolvulus (Py) Clematis (?) Issues: More awareness of oomycetes today formerly some naivety about water testing Disinfection vs. natural biological? More guidance needed May not know when initial problem occurs only see symptoms later - is there a stress trigger? Monitoring visual, lateral flow devices for plants, water, beds? Need development Forecasting seasonal peak, some crops would drench regardless Metalaxyl, Fenomenal, Revus, Pergardo-Uni (mandipropamid) provide control options (and because of potato blight providing market pull for products, a reasonable range is available), but can be too late in application. Also, difficulties arise in finding suitable formulations for HNS in terms of worker exposure/phytotoxicity, etc. 9

10 Conclusions The research needs and actions highlighted by this workshop are as follows: Legislation/enforcement Using diagnostics technology to improve plant health inspections and cut off inoculum at source. Basic Research - BBSRC/DEFRA research opportunities Understand why pathogens behave differently in UK than elsewhere with a view to determining suppressive agents what determines virulence and why does a silent infection become pathogenic? Understanding of damping off in young plants what changes as they mature to make them much more capable of resisting oomycete attack? Breaking dormancy in oospores and luring zoospores to non-hosts Near Market Research potential areas for HDC funding Determine and transfer knowledge to growers for the practical issues involved in both passive and active management of oomycete pathogens in collecting, storing and reusing water. Develop appropriate sampling and monitoring regimes for maintenance of safe practice - workshop needed and substantial knowledge transfer opportunity. Continue to assess extent of contribution of biological control agents; investigate effective use of suppressive material such as green waste Commercial Sector Opportunities: Do whatever it takes to ensure flow of oomyceticides from major agricultural applications; ensure availability of products through attention to worker exposure issues Improved diagnostics to help early detection Seed treatments for control of damping off Plant breeders to incorporate genetic resistance to oomycetes 10

11 Appendix 1 HDC Oomycete Root Disease Research The list below details the sequence of research projects funded by the HDC to directly address the problems that these pathogens cause. Whilst fairly comprehensive it is not exhaustive; several other projects have considered oomycetes alongside a complex of other pathogens. Project No. Title Report Date FV 006 Control of Phytophthora crown rot of parsley 1988 FV 005a Development of a diagnostic test for the pathogens which cause cavity spot of carrot 1993 HNS/PC 058 Protected crops and HONS: rapid diagnostic tests for root and stem base pathogens 1993 SF 023 Crown rot of strawberry: transmission of the pathogen (Phytophthora cactorum) in 1994 micropropagation PC 107 Comparison of chemical disinfectants for treatment of a glasshouse sand bed contaminated with Phytophthora 1995 SF/HNS 037 Detection of Phytophthora diseases in horticultural planting stocks by the polymerase 1996 chain reaction (PCR) FV 207 Lettuce: evaluation of existing and novel fungicides for the control of foliar pathogens 1998 and Pythium root rot PC 097 Identification of sources of inoculum and the development of rapid diagnostic tests for 1998 Pythium infestation of ornamentals on nurseries PC 125 Cucumber: evaluation of disinfection treatments for the control of Pythium spp. in 1998 rockwool slabs FV 226 Red Beet: Investigation into the cause and distribution of root malformation disorder 2001 (RMD) PC 097a Ornamentals : sources of Pythium inoculum fungicide resistance and efficacy of surface 2001 sterilants FV 005f Carrot: the control and biology of cavity spot 2002 PC 157 Chrysanthemums: investigation of propagation techniques to improve plant 2002 establishment, yield, quality and resistance to root-rot pathogens during winter and spring production FV 226a Red Beet: further elucidation of the cause, epidemiology and control of root 2004 malformation disorder (RMD) FV 226c Red Beet: further elucidation of the cause, epidemiology and control of root 2004 malformation disorder (RMD) HNS 123 Control of Phytophthora ramorum in nursery stock (COPRINS) 2004 FV 226d Red Beet: further elucidation of the cause, epidemiology and control of root 2006 malformation disorder (RMD) FV 240 Chicory: control of root rot caused by Phytophthora species 2006 FV 246a Asparagus: Management of Phytophthora rot 2006 HNS 123a Chemical control of Phytophthora ramorum causing foliar disease in outdoor hardy 2006 nursery stock SF 082 Development and evaluation of a real-time (TaqMan (TM)) PCR assay of for detection 2006 of Phytophthora cactorum (crown rot) in strawberry tissue FV 005g Assessing the effectiveness of a Norwegian developed PCR assay for the prediction of 2007 carrot cavity spot levels by measuring soil levels of five Pythium species SF 063 Diagnostic markers for root rot resistant raspberries suitable for low input growing 2007 systems [LINK] SF 078 Meristem culture for the elimination of the strawberry crown rot pathogen Phytophthora 2007 cactorum HNS 134 Detection and decontamination of Phytophthora spp. including those of statutory 2008 significance from commercial HONS nurseries CP 046 Carrot cavity spot: the effects of non-carrot crops on levels of relevant Pythium spp. in 2009 the soil (HDC Studentship) HNS 169 Choisya: surveys of the occurrence of root rotting and potential causes 2009 FV 353 Carrot cavity spot: (i) using quantitative PCR to predict disease in strawed crops; (ii) 2010 controlling soil moisture for optimum disease management FV 352 Disease management in organic Brassica seed and transplants 2011 FV 362 Reducing wastage and increasing shelf life of root vegetables during washing, packing 2011 and retailing FV 373 Carrots: BCGA Incidence of cavity spot in Commercial Crops

12 Project No. Title Report Date HNS 168 Rosaceous trees: Evaluation of treatments for control of replant diseases in Sorbus aucuparia 2011 HNS 181 Survey detection and diagnosis of Phytophthora root rot and other causes of die-back 2011 in conifers PC 281 Protected tomato: monitoring rhizosphere micro-organisms to improve understanding 2011 and management of root diseases SF 099 Sustainable control of crown rot (Phytophthora cactorum) in strawberry 2011 FV 367 Spinach: biology and management of damping-off disease 2012 SF 121 Evaluation of products for control of crown rot in strawberry 2012 FV 391 Carrots: improving the management and control of cavity spot 2014 HNS/PO 188 Baiting and diagnosis techniques for monitoring Phytophthora spp. and Pythium spp. in 2014 irrigation water on ornamental nurseries SF 123 Efficacy of novel products for the control of Phytophthora rubi raspberry root rot 2014 SF 130 Raspberry: Detection and quantification of Phytophthora rubi in soil and in plant tissue