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.