Pangasius ponds
Taking water samples for eDNA analysis

Molecular Biology

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). Such biomarkers could be used in early warning of impending disease outbreaks and so help to alleviate the impact of disease outbreaks in small scale farms.

The basic concept of eDNA is molecular detection of (micro-) organisms without needing to observe, physically identify or isolate them. Whole communities or individual lineages can be detected in a wide range of environments (e.g. water, sediment, biofilms) or biological materials (whole animals, tissues, gut contents, faeces). eDNA methods provide a range of powerful tools relevant to pathogen/parasite discovery, characterization and diagnostics; identification of pathogen reservoirs; abundance and distribution of known pathogens and their relatives; and understanding pathogen assemblages in hosts and local environments. The approach can be general (metagenomic methods), providing information on the whole community through to highly specific,(e.g. PCR-based assays) for identifying individual or groups of closely related pathogens. eDNA approaches can be applied to pathogens already recognized as problems (e.g. white spot syndrome virus; WSSV), as well as those causing undiagnosed syndromes (e.g. running mortality syndrome (RMS), monodon slow-growth syndrome(MSGS)). eDNA techniques can detect all of these, and combined with histology coupled with molecular analyses (‘integrated pathology’) can diagnose and characterize them, providing a diagnostic molecular marker that can be used for ongoing monitoring. We aim to adapt the most inexpensive, robust, and field-friendly eDNA methods for use by individual farmers.