P1904300: AHDB Research Call: Mushrooms - understanding complex microorganism communities to inform the management of priority diseases and promotion of beneficial organisms

Purpose/primary objective

AHDB wish to commission research and appropriate knowledge exchange activities to gain insight into the complex microbial communities including pathogens and beneficial organisms that have an impact in mushroom production. The knowledge generated will contribute to the management of damaging diseases like bacterial blotch of mushroom caused by several species of Pseudomonas and/or green mould caused by Trichoderma aggressivum. The focus will be on the use of new technologies that will lead to developing and testing innovative methods of control.

Research outputs will be used to provide recommendations to growers on best practice to detect the pathogens and control diseases whilst promoting beneficial organisms in order to reduce the losses due to high-risk diseases such as bacterial blotch and/or green mould in UK mushroom production.

Scope

The basis for this call for proposals will be the study of complex microorganism communities and how they manifest into either a healthy or diseased crop, with an emphasis on important diseases like bacterial blotch and/or green mould. Confirmation of the range of pathogens that can cause disease and how these pathogens co-exist in complex communities that include beneficial microorganisms, throughout the different stages of mushroom production need to be validated. The proposed work should lead to the development of accessible and practical diagnostic methods to allow early detection of diseases, before symptoms develop, and also to the development of innovative methods for control that are likely to be approved for mushroom production. We would like to develop an exciting programme of mushroom research and would also welcome proposals for co-funding projects where appropriate.

Background on mushroom bacterial blotch and green mould

Bacterial blotch disease caused by Pseudomonas spp. is the most important bacterial disease problem currently faced by the mushroom industry in the UK and elsewhere in Europe. The disease is favoured by high relative air humidity that can lead to condensation on the caps when temperature fluctuates and ventilation is insufficient. Different Agaricus strains have variable susceptibility to bacterial blotch, so breeding and selecting resistant or tolerant strains might contribute to disease control. The phylogenetic relationships between various Pseudomonas pathogens that cause bacterial blotch including severe, mild and ginger blotch symptoms, is still poorly understood. The early detection of the pathogens is essential for the control of the disease, but there are currently no methods for detection of all pathogens that cause the disease. It is also important to ensure the discrimination of potential pathogens from related beneficial pseudomonads that stimulate initiation of mushrooms and might also suppress pathogenic populations. There are still no practical treatments for bacterial blotch and the disease is generally managed by cultural practices that include reducing the humidity in the growing rooms. The manipulation of the environmental conditions through balancing the temperature, irrigation and ventilation helps control bacterial blotch, though these methods have limitations, are dependent on outside conditions, and can lead to cracking and yield reductions due to high temperatures and low humidity. In some cases, environmental regulation is not effective and disease can spread causing significant loses. Therefore methods for early detection of the disease and strategies for controlling it should continue to be developed.

Two recent AHDB projects have provided new knowledge on this disease: 

  • Project M054 (completed in September 2012) included the study of the development of blotch symptoms in different environmental conditions and the development of a real-time PCR test for Pseudomonas tolaasii, the cause of severe brown blotch, based on the tolaasin toxin gene sequence. This test does not detect Pseudomonas isolates that caused ginger blotch or mild blotch symptoms.

  • Project M063 (completed in April 2018) included a review on the phylogenetics and ecology of blotch causing Pseudomonas Whole genome sequences were generated for representative isolates of P. tolaasii, P. gingeri and other blotch-causing Pseudomonas and a real-time PCR test was developed for P. gingeri. Although strains of P. tolaasii and P. gingeri can be detected by the real-time PCR tests already developed, these tests will not detect a range of strains that cause mild blotch symptoms. Irrigation with a 0.3% solution of CaCl2 reduced the occurrence of blotched mushrooms, but this is not approved for use in the UK, so alternative methods of control need to be developed.

Green mould caused by the fungus Trichoderma aggressivum f. europeum can cause severe mushroom crop losses in the UK and a different form, T. aggressivum f. aggressivum has caused significant losses in North America and remains a threat for the UK. In addition, two other species T. harzianum and T. atroviride are present in the UK, but do not generally cause economic losses. In 2013, it was estimated that the cost of green mould to the UK mushroom industry could be £0.5M – 1.0M annually (M 57, final project report). Green mould is generally controlled by compost pasteurisation and sanitation measures including the use of disinfectants, but it is difficult to achieve eradication of the pathogen and some disinfectants leave residues and therefore should be used only where they are unlikely to come in contact with the crop or substrates. Although prevention has to be central to avoid this disease, when the infection occurs in a producing facility, appropriate strategies for control should be in place.

Previous AHDB projects on detection and control of green mould:

  • Project M 048 (completed in 2010) included the development of DNA extraction methods for Trichoderma from Phase III compost and the development of a real time PCR using the translocation elongation factor gene to detect T. aggressivum. This method does not discriminate between T. aggressivum f. europaeum (Th2) and f. aggressivum (Th4).

  • Project M 050 (completed in 2011) showed that T. aggressivum is extremely temperature tolerant requiring compost pasteurisation conditions of 60°C for 12 hours to eradicate the pathogen; survival declined with increasing ammonia concentration. The real time PCR detection method developed by FERA was tested to detect T. aggressivum in phase III infected compost.

  • Project M 057 (completed in March 2013) looked at the influence of ammonia during compost pasteurisation and disinfectants on eradication of T. aggressivum. In this project, combinations of selective plating and real-time PCR were successfully used to detect T. aggressivum. The use of appropriate pasteurisation conditions reduced the occurrence of the disease from compost. Although none of the tested disinfectants completely eradicated Trichoderma inoculum in infected compost, some disinfectants reduced infection levels and/or suppressed growth.

Other relevant publications

Fermor et al., 1991. Development and application of a biocontrol system for bacterial blotch of the cultivated mushroom. Crop Protection, Vol 10 (4): 271-278

Navarro, M.J. et al., 2018. Identification, incidence and control of bacterial blotch disease in mushroom crops by management of environmental conditions. Scientia Horticulturae, 229: 10-18.

O’Brien et al., 2017. Detection of Trichoderma aggressivum in bulk phase III substrate and the effect of T. aggressivum inoculum, supplementation and substrate-mixing on Agaricus bisporus yields. European Journal of Plant Pathology, 147: 199-209.

Milijasevic-marcic, S. et al., 2017. Biological control of green mould on Agaricus bisporus by a native Bacillus subtilis strain from mushroom compost. European Journal of Plant Pathology, 148: 509-519.

Specific objectives

1. Study of microbial communities

Diversity and abundance of pathogens and potential beneficial organisms

A study of the populations of microorganisms associated with healthy and diseased crops, sampled at different stages, should provide information on levels of potential pathogens and potential beneficial organisms associated with mushroom production.

Genes involved in pathogenicity and/or other genes that are useful for identification and discrimination of different pathogens like Pseudomonas that cause bacterial blotch and Trichoderma associated with green mould, and also discrimination of the pathogens from possible beneficial organisms, should be selected. This should also build on information obtained in previous projects and can use existing genomes already generated and/or include new sequence information from a range of organisms. All genomic data should be made publicly available in a suitable and accessible data repository.

2. Pathogen detection

Develop and test methods for early detection of the pathogens involved in disease

New or existing methods should be developed or expanded for practical and inexpensive early detection of pathogens in substrate, casing and in mushroom crops. This will be essential to pinpoint the sources of infection. A tool/service for fast and early identification of the pathogens should be tested. 

3. New Control measures

Develop and evaluate new methods for controlling bacterial blotch and/or green mould

AHDB will welcome new ideas for methods of control that could include, but not limited to, biological controls and use of bacteriophages together with appropriate management of environmental growing conditions. Any new proposed methods must be likely to be approved and accepted in commercial mushroom growing practices.

4. Knowledge Exchange

The outputs listed below are considered a minimum; potential contractors are encouraged to outline other relevant knowledge exchange activities for industry. 

  • Annual and Final reports to AHDB

  • All genomic data and markers should be made publicly available in a suitable data repository.

  • Article for AHDB Grower magazine

  • Oral presentation at relevant grower events (to be agreed with additional associated costs)

Project duration and budget

The indicative budget is in the range £100 k (excluding VAT) for a project period of two years (there is scope to extend funding if part of a co-funding initiative or appropriate PhD proposal). AHDB would be keen to receive proposals that demonstrate the following: Skills and capacity building for the mushroom industry; an understanding for how the proposed project aligns within the wider, national and international mushroom research community and how this will benefit the UK mushroom industry.

Collaboration

Prospective contractors are encouraged to submit a joint proposal if complementary expertise has been identified. AHDB may, if it is deemed desirable, request applicants to form a project consortium.

Completion and submission of the application form

Applicants should complete an AHDB Research and KE Application Form – Full Proposal Large, referring to the guidance notes to aid completion. 

Applications are made on the basis of the AHDB Research Funding Agreement and any organisation receiving funding shall comply with the terms and conditions specified in the RFA. AHDB will not be held responsible for any expenses or losses incurred by applicants in the preparation of an application(s).

Completed application forms should be submitted to research@ahdb.org.uk no later than 12:00 noon on 24 May 2019.

Proposed timings for application and project delivery

Call Published

16 April 2019

Full Proposal deadline

12:00 noon on 24 May 2019

There is no Concept or Expressions of Interest phase.

Make an electronic submission to research@ahdb.org.uk 

Receipt will be the time of receiving email.

Applications reviewed and applicants informed of outcome

14 June 2019

Project commences

10 September 2019

Project completion

30 September 2021 (2 years)

If you have specific questions relating to this call, please email research@ahdb.org.uk 

As part of the open tender process, AHDB cannot discuss specific programme details prior to proposal submission. All Questions & Answers will be published.

Assessment criteria

Please note that the assessment criteria have been slightly altered for this tender, please see below. 

Project Title:

Mushrooms: understanding complex microorganism communities to inform the management of priority diseases and promotion of beneficial organisms

Applicant:

SECTION 1: PROJECT OVERVIEW (Not assessed)

SECTION 2: PROJECT OUTCOMES Beneficiaries appropriately identified. Novel approaches to deliver industry KE and links to existing AHDB KE activities. Appropriateness and clarity of industry engagement. Timeframe qualified to deliver project outputs and impact. Clarification over additional activities/resource required to deliver impact. Environmental benefits appropriately identified and any negative impacts detailed. Key Performance Indicators identified. Clear IP exploitation plan and route to commercial development where relevant. 0-10 score; weighting of 3

 

 

 

Score:        x3 =

SECTION 3: TECHNICAL APPROACH AND WORK PLAN Evaluation of current knowledge (appropriate references used) and awareness of other work. Clarity of aims, objectives, work packages and milestone schedule. Originality & innovation. Effective collaboration with commercial companies and relevant research organisations. Is the approach statistically robust? Feasibility and risk management. Project management structure and responsibilities clearly defined.  0-10 score; weighting of 3

 

 

 

Score:        x3 =

SECTION 4: RELEVANT KNOWELEDGE AND EXPERTISE Quality of past contributions to, and impact on, the topic demonstrated. Potential to bring added value through current and/or past contributions. Complementarities of expertise of the team and roles of collaborating organisations (if relevant) clearly defined.  0-10 score; weighting of 2

 

 

 

Score:        x2 =

SECTION 5: PROJECT COSTS Are costs reasonable and necessary? Will the total budget be adequate to carry out the proposed activities? For a cross-Sector proposal, is the shared budget appropriate & clearly defined? Added value of co-funding? 0-10 score; weighting of 2

 

 

 

 

Score:        x2 =

Total Score            out of 100   (Threshold = 50)

Recommend for Funding           Yes / No