Aerial Oomycetes – development of integrated management strategies

Aerial Oomycetes – development of integrated management strategies

Background

Aerial oomycete pathogens include Peronospora spp., Pseudoperonospora spp., Plasmopara spp., Phytophthora spp., Bremia lactucae and Albugo spp. Diseases caused by these pathogens such as downy mildews of vegetable and ornamental crops, and late blight in potato and tomato, can develop rapidly under optimal conditions, resulting in crop losses ranging from moderate to total, often in very short periods following initial infection. Control of these diseases using fungicides alone can be problematic for the following reasons, i) changes to legislation and the approvals process has led to a reduction in the availability of new and existing conventional fungicides and biopesticides, particularly for minor crops, ii) aerial oomycetes do not readily respond to eradicant fungicide applications, thus disease management often requires prophylactic sprays and iii) development of resistance to certain fungicides such as metalaxyl-M, can develop rapidly, particularly when limited alternative modes of action are available. Use of resistant varieties is an ideal strategy for disease control in the long-term, however, continual development of pathogen races that can overcome host resistance (eg. Bremia lactucae on lettuce and Peronospora farinosa f. sp. spinaceae  on spinach) or that are particularly aggressive (new races of Phytophthora infestans on potato and tomato), mean that disease outbreaks can still occur. Overall, integrated management strategies for aerial oomycetes need to incorporate cultural methods (eg. crop hygiene, manipulation of environmental conditions) alongside judicious use of fungicidal control together with durable host resistance where available.

AHDB has previously funded a wide variety of research and knowledge exchange activities designed to inform growers and agronomists and offer control options (see 6. Related Information).  However, in a number of crops, diseases caused by aerial oomycetes continue to cause economic impacts. 

Purpose/Primary Objective

The AHDB wish to commission research and knowledge exchange that will provide information and opportunities to reduce the economic impacts in the short, medium and longer-term regarding diseases caused by aerial oomycete pathogens in a wide range of UK crops.

Scope

Aerial oomycetes cause disease on crops within all UK horticultural sectors (except tree fruit), as well as potatoes. Therefore, project outputs and outcomes relevant to a wide range of crops are expected. Table 1, in section 6, provides information regarding the relevance of this work to various crop sectors. It is, however, anticipated that a ‘model crop’ approach will be required for some aspects of the work. This should always ensure that relevant crop environments/types are considered eg. protected/field production, ornamental/edible crops.  Due to the continuing impact of certain diseases on production, it is expected that some research activities will be focused on specific host/pathogen targets. Certain defined aspects of this call are also relevant to potato crops. 

Work on crops such as hops and grapes is not included in this call.  Proposed work should be focused on aerial oomycetes only, and not include root, crown or collar rot pathogens in this instance. 

Collaboration and co-sponsorship

AHDB may, if it is deemed desirable, request applicants to form a project consortium.

For certain work packages, priority will be given to the applicants with cash and/or in-kind funding from alternative funding bodies, or commercial partners.

Specific Objectives

WP 1: Pathogen biology and disease epidemiology

Objective 1: Review and collate information on pathogen biology and disease epidemiology for aerial oomycetes, in order to inform the development of integrated management practices.

For many aerial oomycete pathogens, there is a wealth of information available from scientific literature and research reports on pathogen biology and disease epidemiology that could inform grower practice and aid the development of better management practices. The review should collate information on the following aspects (not necessarily exhaustive) and highlight clearly where information could be used immediately by growers to improve disease management, and/or could provide the basis for future cultural control methods or decision support systems; knowledge gaps should also be identified:

  • Sources of inoculum, pathogen life-cycle, spore types and survival

  • Role of seed-borne inoculum in disease transmission (internal/external infestation, likelihood as primary route for infection)

  • Existing decision support and forecasting tools, and scope for use in the UK

  • Existing diagnostic methods for the pathogen in/on seed, in soil and water and on plant material and scope for further development either as research tools and/or on-site diagnostics

Priorities: Downy mildews on lettuce, spinach, rocket, onion, peas, tomato blight, and key affected hosts of herbs, hardy nursery stock and ornamentals, eg the newly emerging species on column stocks.

Key outputs:

  • Knowledge review and findings in the form of a report to AHDB and incorporation into the output for WP 6 below.

Objective 2: Develop methods for pathogen detection in seed, and determine the importance of seed-borne inoculum in transmission of aerial oomycetes

AHDB has previously, and continues to fund work in this area, eg. on impatiens (PC 230), basil (PE 024) and red beet (FV 226). A limitation to this research has been that routine molecular detection methods (eg qPCR) quantify non-viable in addition to viable pathogen DNA, such that it is difficult to draw conclusions about the role of seed-borne inoculum, transmission and risk thresholds. Research on spinach downy mildew in the USA (Klosterman et al., 2017) shows that valuable insights into disease epidemiology can be made where methods for detection of viable oomycetes are used. Clearly this is a rapidly developing area with the emergence of new high throughput technologies for pathogen detection and the need for appropriate sampling methodologies.

Contractors are asked to propose and validate approaches that could complement and advance recent and ongoing research (worldwide) to better understand the role of seed-borne inoculum in transmission of aerial oomycetes in the UK.

Priorities: The suggested focus would be Peronospora farinosa f. sp. spinaceae (Pfs) (= P. effusa) on spinach (oospores known to occur), Peronospora belbahrii on basil (no oospores detected to date) and the downy mildew currently affecting column stocks.  It is suggested that these are used for a ‘model’ crop approach, but that the methods developed could be relevant to the majority of crops where downy mildew species are detected.

Key outputs:

  • Development or adaptation of appropriate research tools/technologies to provide cost-effective methods for quantifying the importance and viability of seed-borne infections.

  • Use the tools and technologies above to determine the role of seed-borne inoculum in UK downy mildew outbreaks for spinach and basil.

  • Information and results to be provided in AHDB report format, with appropriate knowledge exchange.

WP 2: Cultural control

Objective 1. Review and evaluate cultural control methodologies that manipulate the protected environment for control of aerial oomycetes in propagation and protected crops

To include:     

  • Relative humidity (RH)

  • Ventilation

  • Use of thermal heating

  • UV-B and UV-C and manipulation of other light wavelengths

  • Night break lighting

Recent research has shown the potential to reduce downy mildew sporulation using a range of lighting technologies (including UV-C, UV-B, manipulation of light wavelengths and night-break lighting), whilst additional research on RH, ventilation (to reduce dew point and leaf wetness periods) and the use of heat to kill mycelium and reduce spore viability have all shown value in a number of crops.

Key outputs:

  • A review of information and results from recent global research on the effects of the cultural techniques named above, and others that may be of value, for the control of downy mildew in protected crops, with direct relevance to basil, pot herbs, aquilegia, viola, stocks, protected salad crops.

  • Where there is insufficient available information on the relevant crops, contractors are asked to propose research that could be done to complement and advance recent and ongoing studies (global) using lighting technology for downy mildew control.

  • Results and output to be provided as part of an AHDB report and incorporated into main knowledge exchange output (WP6)

Objective 2. Review and compare known and novel methods for reducing dissemination of or destroying infectious propagules (oospores, zoospores, sporangia, conidia) in irrigation water, crop debris, soil and growing media.     

There has been extensive past research investigating and evaluating techniques for reducing the risk of dissemination of aerial oomycetes in water and via a number of other mechanical routes.  It would be valuable to consider past work and add any new information and methods to this information.  Additionally, for growers to understand the importance of the various routes for infection and be provided with a range of useful strategies, from a time and cost perspective, is considered of value.

Key outputs:

  • Review current and new information for control of infectious propagules in water, crop debris, soil and growing media.

  • Compare the techniques for efficacy, cost, and time inputs required.

  • Collate information with specific relevance to salad crops (lettuce, radish, spinach, rocket), salad onion, tomato, peas, ornamental crops (poppy, Geum, Aquilegia).

  • Results and output to be provided as part of an AHDB report and to be incorporated into main knowledge exchange output (WP6) 

WP 3: Use of fungicides and biofungicides as components of IPM programmes

Objective 1. Develop IPM programmes for aerial oomycetes using currently approved products and new approvals identified in SCEPTREplus, to include seed treatments, and conventional and biological fungicides timed according to disease risk/pressure, and with particular attention to incorporation of strategies to avoid the development of fungicide resistance.

Whilst many of the larger businesses use agronomists and consultants to develop effective fungicide strategies for their crops, many of the medium to small organisations do not.  For these growers in particular, trying to keep their knowledge of product approvals up-to-date for a number of crops can be challenging.  Added to this, the knowledge of whether products are systemic or non-systemic in their activity, protectant or eradicant, and whether their proposed regime includes the best products to minimise fungicide resistance risk (contains a range of FRAC codes) can be a particularly difficult task.  Support, in the form of updatable IPM programmes is considered a high priority.

It is anticipated that the contractor will liaise closely with AHDB staff regarding SCEPTREplus product testing and anticipated approvals (EAMUs) to ensure this work is up to date and relevant.

Key outputs:

  • Development of effective and targeted IPM programmes which minimise resistance risk for a range of key crops to include outdoor and protected leafy salads (lettuce, spinach, rocket, radish), outdoor herbs, peas, field beans, Impatiens, viola/pansy, rose and Hebe.

  • Information to be provided as crop-specific information sheets which can be used electronically or as hard copies.

Objective 2. The development of a service to monitor fungicide sensitivity in key aerial oomycete pathogens eg Bremia lactucae, Pfs, Peronospora viciae, and Phytophthora infestans (tomato)

Insensitivity to key active ingredients used for control of the above pathogens is already known to occur. In potato crops the development of genotypes of P. infestans with insensitivity to fluazinam is of major concern to the industry, and a similar situation with mefenoxam insensitivity in Bremia isolates is also well reported.  The development of a service to allow growers and farmers to check the fungicide sensitivity of isolates of the aerial oomycete pathogen present in their crop would be of value. Within the lifetime of this project, it is anticipated that up to 20 isolates from each pathogen/crop group would be tested, providing timely information to growers during that growing season.  However, it is envisaged that this information could also feed into a useful national monitoring service to be orchestrated and run by the successful contractor following completion of this project.

Key outputs:

  • The development of fully validated laboratory tests to determine the fungicide sensitivity of up to 80 pathogenic isolates per year to 3 key fungicides per crop.

  • Knowledge exchange activity to report these findings (anonymously) for the greater benefit of the relevant industries.

  • The intention to develop a commercial service to continue testing for growers following the end of this project.

WP 4: Diagnostics and decision support

Objective 1.  Development of a tool/service for faster identification of existing and developing races of downy mildews (lettuce and peas)

Race testing and identification of Bremia genotypes in lettuce crops relies primarily on testing of isolates against differential sets of the specific crop which contain known resistance genes. This system is relatively slow, and not always conclusive.  No similar system is available for the development of new races in peas.  Alternatively, genotypes of Phytophthora infestans infecting potatoes and tomato are able to be tested using a fully validated molecular test. 

AHDB are interested in the potential development of a similar test for Bremia and pea downy mildew. These tests could then be developed into commercially available services for growers and farmers to access as required.

Designation of new races of Bremia is coordinated by the International Bremia Evaluation Board (IBEB) and confirmation and agreement of race development in lettuce will need to be done in concert with this group. This will be the responsibility of the contractor. 

This component of the work is anticipated to require significant investment and therefore AHDB will seek to co-fund into a larger project, or alternatively, to expect the proposer to seek additional funding from other interested parties eg seed producers.  A contribution of £20,000 is available towards this work.

Key outputs:

  • The development of a fully validated molecular test to identify isolates of Bremia and viciae to race level.

  • The provision of such a test for up to 20 isolates of each pathogen per year for the duration of this project (20 isolates x 2 pathogens).

  • Knowledge exchange activity to share the results with individual growers, but also via the AHDB website for the benefit of the wider industry.

  • The intention to develop this as a commercial service to growers following the end of this project for lettuce and pea growers. A service for provision of outbreak information for late blight in potatoes already exists: https://potatoes.ahdb.org.uk/online-toolbox/fight-against-blight-tool and it is anticipated that a separate specification for provision of a late blight service will be issued in due course. For added value this may include provision of this service for tomato growers also.

  • An annual résumé of the findings from the tests carried out as part of an AHDB report.

Objective 2.  The development of real-time disease risk monitoring

Development of disease-risk monitoring or decision support systems is now a real possibility in a number of crops affected by air-borne propagules from pathogens such as Mycosphaerella brassicicola and yellow rust. Quantification of spores linked to environmental models to provide disease-risk ratings are considered of value to many growers and farmers who are interested in gathering data which could help them make decisions about when to apply control measures (fungicides) to their crops.  This could be to avoid unnecessary use of fungicides, or allow them to target sprays with an appropriate mode of action when a limited number of applications are permitted.  AHDB are currently funding some work of this type in the vegetable, potato and cereals sectors. For Bremia, extensive work has already been done on forecasting systems for lettuce (eg Bremcast) and there has been recent progress in the US with quantification of airborne spores (Klosterman et al., 2017).   However, there is scope to extend this into other crops where additional benefit could be gained. Development of this type of system, culminating in a commercial service for growers to gather and share risk data on a national level, is anticipated to be lengthy and costly and is likely to extend beyond the duration of this project.  Therefore, we are interested in working with contractors who are seeking co-funding from AHDB as part of a larger project. A contribution of £30,000 is available towards this work.

Key targets for this work are, for example: Bremia in lettuce, or downy mildew in bulb/salad onions. Although a current project (FV 456) is already delivering a package of work on onion, the potential to build on this to link into a national disease risk system is of great interest. Opportunities to extend into other crops, for other pathogen/host combinations may also be of interest at a later date.

Desirable opportunities and outputs:

  • The opportunity to co-fund a larger project which offers opportunities for AHDB crop sectors to be represented in decision support system development.

  • AHDB representation in the development phases of a larger project.

  • Knowledge exchange to inform levy payers of system development, delivery etc.

WP 5: Host-plant resistance

Objective 1. Collate information regarding the use of elicitors or similar which have the capacity to activate the plant’s own internal defence mechanisms against aerial oomycete pathogens.

Whilst there appears to be a good body of knowledge on the efficacy of a number of elicitor type products for controlling aerial oomycetes in a range of crops, under the current regulatory framework it seems likely that these will not gain approval as plant protection products in the very near future.  AHDB would, however, value a review of current knowledge for our growers and farmers in key cropping areas.

Key outputs:

  • A short review of the literature surrounding the use of elicitors for controlling aerial oomycetes on relevant key crops to be provided in AHDB report format. Key crops: Leafy salads, onions, ornamentals, tomato and potatoes.

Objective 2. Develop novel approaches for downy mildew resistance breeding

AHDB wish to co-fund research groups who are seeking funding via larger BBSRC or EU projects to use novel breeding techniques to either disrupt the infection process in plants, or build robust host resistance strategies in key crops (lettuce and spinach). The goal would be to avoid the repeated breakdown of gene-for-gene resistance that makes sustained disease management through host resistance so difficult to achieve at present. This type of activity can offer the contractor the benefit of being able to demonstrate industry support for the work, and provides AHDB with a route to leverage funding against projects normally outside the scope of the organisations.  A contribution of £50,000 is available towards this work, ideally to co-fund two larger projects.

Whilst growers recognise that this type of research brings benefits in the future rather than now, they do see the value of such work that can ultimately result in varieties that provide sustained host plant resistance and the ability to manage crops with less reliance on fungicides.

Strong collaboration with relevant seed companies (plus co-funding) would be expected as part of this work, to ensure that technologies developed could be incorporated into commercial breeding programmes.

Key outputs:

  • Knowledge exchange activity which introduces the project, and updates growers on key findings and outcomes as the work progresses via a steering group involving industry members.

WP 6: Knowledge Exchange

A number of specific knowledge exchange activities are identified under some of the work packages described above. Excellent knowledge exchange is a key component of this project.  Demonstration of novel and innovative types of delivery will be anticipated, for example, the use of webinars, online discussion forums, the use of social media, YouTube clips etc, alongside our more formal reports, factsheets and articles.  

In addition, this work package includes the following objective:

Objective 1. Incorporation of relevant findings from completed work packages into ‘Best Practice Grower Guides’ for management of downy mildews on selected crops

AHDB would like the successful contractor(s) to develop a set of ‘Best Practice Guides’ for the management of key crops to incorporate findings from work packages 1 (O1), WP2 (O1 and O2) specifically, but also other crop relevant information collected within the course of the project.

The guides should provide information for a range of strategies for avoiding or controlling aerial oomycetes on key crops (see below) in a logical format eg from seed to harvest and between- crop hygiene.  The guides should be provided in a number of useful formats eg in hard copy for AHDB in-house publication, as electronic versions downloadable on smart phones, and potentially as webinars or video clips.

Key crops: Lettuce, spinach, rocket, protected and outdoor herbs (parsley, sage, mint, coriander), salad & bulb onions, brassicas (in propagation only), peas, Aquilegia, Viola, Hebe, Impatiens, stocks, rose

Key outputs:

  • Collation of information from previously described work packages into Best Practice Grower Guides in a number of formats

WP 7: Project Management

Due to the wide range of work packages and complex nature of this project, AHDB are seeking the services of an organisation to take on the role of project management.  Ideally, this will be considered by a contractor also bidding to complete one or more of the work packages identified in this specification.

The role of the Project Leader will be to monitor other work packages for quality and delivery, liaison with AHDB via Project Steering Group meetings, which will include levy payer representatives from a range of crop sectors, co-ordination of knowledge exchange activities and collation of reports from separate work packages into one annual or final report.   

Related information

Research and development work, particularly in the diagnostic and forecasting areas, is currently ongoing using Innovate UK funding.  Additional research to understand the mechanisms of infection pathways for oomycete pathogens and resistance mechanisms is also underway in a number of countries (including seed company confidential research).  Work on this group of pathogens has also being undertaken by IR4, or recently within CORDIS and C-IPM.

Table 1. Previously funded AHDB work aerial oomycetes

Project Number

Title

CP 157

Aerial Oomycetes - review of management and control options available for the UK horticultural industry

CP 077

SCEPTRE

CP 099c

Bulb and Salad Onions: Evaluation of an integrated disease management system to ascribe the risk of downy mildew disease on commercial crops in the UK.

CP 165

SCEPTREplus

FV 390

Outdoor herbs: epidemiology and control of downy mildew in sage, parsley, mint and basil under protection

FV 436

Pea: Downy mildew diversity in the UK

HNS 150

Managing downy mildew epidemics in rose by early detection and treatment of infection sources

HNS 173

Epidemiology and prediction of rose downy mildew

HNS 186

Control of downy mildew on rose and herbaceous plants

HNS 196

Identification of inoculum sources for the newly emerged Peronospora causing downy mildew on aquilegia

PC 230

Detection and control of downy mildew on ornamentals

PC 230a

 

Control of downy mildew (Plasmopara obducens) an economically important foliar disease on Impatiens

PC 230b

Source of downy mildew (Plasmopara obducens) infections on Impatiens

PE 024

Basil: Improving knowledge and control of downy mildew in protected and outdoor crops

PO 011/b

Monitoring metalaxyl-M sensitivity in Impatiens Downy Mildew isolates from 2012 infections

PO 012

Evaluation of the efficacy of non-metalaxyl-M based fungicides/ programmes against metalaxyl-M resistant strains of Plasmopara obducens

AHDB Horticulture Knowledge transfer covering this topic

Factsheet

 

21/15

Testing water for plant pathogens

22/15

Methods of water treatment for the elimination of plant pathogens

These reports and publications are available from the AHDB Horticulture website horticulture.ahdb.org.uk

Crop relevant information

Information collated from previously commissioned gap analyses in crop protection and from relevant industry priority documents provide a useful starting point for contractors wishing to develop work for this call.

Table 1.  AHDB crop specific targets

Sector

Crop

Pathogen

Priority

Potatoes

Potato

Phytophthora infestans

High

FV/PE

Lettuce

Bremia lactucae

High

FV/PE

Spinach, rocket & other baby leaf

P. farinosa f. sp spinaceae and others

High

FV/PE

Herbs: Basil, Mint, Coriander, Dill, etc.

Various

High

PE

Tomato

Phytophtora infestans

High

FV

Bulb/Salad onion

Peronospora destructans

High

FV

Squash/courgette

Pseudoperonospora cubensis

Medium

FV

Brassicas in propagation

Hyaloperonospora brassicae

High

FV

Field brassicas

Albugo candida

Medium

FV

Broad beans

Peronospora viciae

High

FV

Peas

Peronospora viciae

High

FV

Radish

Hyaloperonospora parasitica

High

PO

Aquilegia

Peronospora sp.

 

PO

Impatiens

Plasmopara obducens

 

HNS

Hebe, Geum, Papavaer, etc.

Various

Medium

Budget and duration

A maximum budget of £294,000 has been allocated for this project, which has a duration of three years. Of this total £100,000 has been allocated to the co-funding opportunities identified in WP 4, Objectives 1 & 2, and WP5, Objective 2.  Applicants will be able to advise on the costs of their proposed work and should calculate and provide the costs attached to their proposal, ideally this should include an indicative cost breakdown for individual work packages.  AHDB reserves the right to consider budget limits and constraints when assessing submissions and may choose not to make an award if submitted ideas prove unaffordable at this time within the context of the wider programme of AHDB work. 

Completion and submission of the application form

Please refer to the guidance notes for completion of application forms. Applicants should complete the AHDB Research and KE Application Form - Full Proposal Large, completed forms must be emailed to research@ahdb.org.uk no later than 12.00 noon on 2 October 2018.

Proposed timings for application and project delivery

Stage of process

Deadline

Call published

19th July 2018

Full proposal submission deadline

2nd October 2018

Applicants informed of the outcome

19th October 2018

Anticipated start date

1st December 2018

Project duration

Three years (ending 30th November 2021)

Questions

If you have a specific question related to this call, please email research@ahdb.org.uk. As part of the open tender process, AHDB cannot discuss specific project details with you before submitting your proposal. Answers to specific questions will be posted on AHDB’s procurement webpage. View the Questions & Answers for this Research Call.

Assessment criteria

Please note that the assessment criteria have been slightly altered for this tender. To access the revised criteria please click here.