Novel Molecular Approaches for Advancing Prediction and Mitigation of Disease Outbreaks in Aquaculture for Small Scale Farmers

Aquaculture contributes significantly to global food security and poverty reduction. In Bangladesh and India shrimp culture sustains the livelihoods of hundreds of thousand of poor people. Finfish culture too is fundamental to the lives of small scale farmers in India and in developing countries around the world, including Bangladesh and Malawi. Disease is the biggest single factor limiting growth in aquaculture (with associated annual losses estimated at >$6bn globally) and combating disease is critical for both the protection of the livelihoods of small scale farmers and for achieving national /global targets for aquaculture growth in support of poverty alleviation.
The proposal will develop and apply of modern molecular methods for use as early warning tools for the avoidance of disease outbreaks in low income food deficit countries. Our central theme is the alignment of the efforts of farmers, Aquatic Health Professionals, researchers and national Competent Authorities to help avert disease outbreaks.

Disease and health status of host organisms is not determined by individual pathogens alone, but by a combination of local abiotic and biotic factors including the environmental microbiome, pathogen assemblages, and pathogen loads in host tissues. We will apply and develop molecular biology methods to identify pond microbiome conditions and biological indicators ('biomarkers') associated with health status and disease outbreaks in key crop species (shrimp and finfish) in aquaculture ponds in India, Bangladesh and Malawi. We will identify pond microbiomes that signal for an impending disease outbreak. We will furthermore determine how the microbiome relates to a variety of pond variables, including the use of probiotic treatments currently used by farmers to improve crop health and increase yield. Models will then be developed using these data and applied to predict the drivers of disease outbreaks.
We will use this information to develop simple but accurate molecular assays for use by farmers on individually-owned farms, enabling them to pre-empt and avoid the impacts of disease events by intervention methods triggered by monitoring carried out on-site. Development of an inexpensive but accurate early-warning measurement of pond/crop health status will demonstrate proof-of-concept for a set of tools/methods that can be applied more widely and further developed by industry investment.

We will engage and train farmers in accurate disease diagnostics and in the importance of managing the microbial-molecular aspect of pond aquaculture and host health, and establish communication and training networks that will disseminate the outputs of the project to other farmers, communities, and research centres working with them, with an emphasis on engaging women. Communication conduits will include Mobile APPs, focused local workshops, information videos, social media and a designated project website. We will assess the impacts of our project for small scale farmers on disease mitigation and crop enhancements adopting DFID's Livelihood Framework for assessing the impacts of agricultural technologies in developing countries.

Our proposal addresses the GRP Aquaculture Call priority areas of Healthy and nutritious aquaculture, seeking to understand, manage and mitigate for some of the most important diseases in aquaculture, in turn increasing productivity for the health and well being of poor small scale farmers. Our proposal is also relevant to the GRP priority area of resilient aquaculture as the ability to predict disease outbreaks will allow for harvesting at an earlier time point before disease onset and/or other interventions to prevent crop loss for small scale farmers. The project proposed furthermore is relevant to the strategic research priorities of various national Research Council and government initiatives relating to food security and poverty alleviation.

Environmental DNA (eDNA) methods will be applied to identify pond microbiome conditions and biological indicators (' molecular biomarkers') associated with health status and disease outbreaks in key crop species (shrimp and finfish) for use in early warning to avoid impacts of disease outbreaks in small scale farms.

Sequenced metagenomes (via Illumina sequencing) of environmental samples will be correlated with host infection status and pathogen diagnoses (via histology/sequencing) for ponds across India, Bangladesh and Malawi. Environmental samples collected temporally for crop species (together with observational data) will be used (incl. modelling) for assessments on how pond and host microbiomes change before, during, and after disease outbreaks for the identification of microbial indicators of host and pond health status and as predictors of disease outbreaks.

Experiments will establish how probiotic treatments used to improve crop health and increase yield impact on the pond (eDNA) microbiomes and disease prevalence.

Recombinase Polymerase Amplification (RPA) assays will be designed for biomarker lineages to determine their sensitivity for detecting these lineages in environmental and organism-derived samples.

Molecular biomarkers of disease risk (together with other observational data) will be communicated to an extensive network of small scale farmers across India, Bangladesh and Malawi for application to assess their value in mitigation strategies to prevent crop losses.

Communication systems will be set up for the exchange of data and knowledge between the project investigators, local research institutes, and individual farms including via APPs, histoPATHway, Facebook, twitter, and a dedicated project website.

Impacts of our project for small scale farmers on disease mitigation and crop enhancements will be undertaken adopting DFID's Livelihood Framework for assessing the impacts of agricultural technologies in developing countries.

Ninety percent of global aquaculture is centred in Asia, most of which is in Low Income, Food Deficit Countries (LIFDCs) where disease outbreaks of endemic pathogens are the biggest single threat to food security and poverty alleviation relating to aquaculture. Improving disease prediction within aquaculture in small scale farms can lead to higher, more consistent, yields with immediate and direct benefits to low level income farmers. Our proposal aims to combine ground-truthed emergent technologies (molecular assays, gene sequencing, smartphone apps) with farmer-led environmental diagnostics to engender a grass-roots approach to biosecurity.

Developing the farmer-AHP-scientist interface in this partnership, expanding on current activities in India, will help develop the most effective surveillance strategy empowering farmers to adopt best disease management practise and a predictive basis for intervention strategies with direct benefits to their own livelihood. Efforts to mitigate poverty associated with outbreaks will furthermore have benefits at national governmental level by promoting rural livelihoods and by alignment with international objectives in food security and biosecurity. The project partners assembled traverse government and academic sectors with a collective influence over policy at the national, EU and inter-governmental levels.

Partner networking and exchanges will directly enhance organisational-level knowledge/skills exchange via training of partner research institutes in biosecurity, pathology, eDNA techniques, metagenomics, non genomic sequencing, RPA development for field use, environmental diagnostics and decision-making. UK researchers will gain specific understanding of social barriers to outbreak avoidance in real world settings. Working with commercial partners in decentralised field diagnostics, we will identify opportunities for production of rapid and economically viable molecular kits to assess pond health beyond the life of this project.

Engagement with the research proposed will centre on a series of workshops in partner home countries and specific farmer/AHP events in India, Bangladesh and Malawi. These events will engage stakeholders in the concepts inherent to the project, to summarise technologies and reporting models to be deployed, to identify key farmer/AHP contacts for pilot testing of concept and to broaden communications to the wider community (local universities, schools, authorities). We will engage local contacts in ensuring appropriate gender balance issues are addressed. Lead partners in formation of the Global Pathology Network (India/UK) will conduct training events, aimed at local AHPs for the purpose of generating competence in this skill focused on Bangladesh and Malawi.

The project is expected to generate numerous peer-reviewed publications that will engage further academics in our work. All teams will present the project through their education programmes that include web and physical outreach initiatives, and to local schools. We will also seek media engagement, as and where appropriate, to broadcast our project in all its facets. In addition, we will produce policy-related documentation, field protocols, and further farmer-oriented guidance documents (and videos) to assist data collection and field management of outbreaks within and beyond project life. The project website (linked through social media) will be the main portal for communication to partners, farmers, AHPs and country-specific Competent Authority contacts. Via secure login, it will also serve as the data repository for information emerging in-country. The overall project team, coordinated by the Project PI, will meet face-to-face at engagement events, annual meetings and during other fieldwork visits. In addition, regular meetings via Skype/teleconference will occur and will attempt to maximise contact and collaboration with other projects funded within this programme.