ENVIRONMENTAL DNA (eDNA) AS FORENSIC TECHNIQUE TO DETECT PATHOGENS IN AQUACULTURE SYSTEMS

Food security will be one of the biggest challenges for humanity as the global population nears 9 billion. Aquaculture, as the fastest growing agribusiness in the world (annual production of 73.8 million tonnes and sale value of US$160.2 billion), is shaping to be a major supplier of humanity's future animal protein needs. However, 40% of current aquaculture production is lost due to diseases. The risk of economic loss due to disease outbreaks can be catastrophic and constrains the continued growth and profitability of the sector.

DNA-based detection technologies linked to environmental data have the ability to accelerate the response of farmers to diseases. It can do this by providing farmers with an understanding about the number of pathogens and how their population dynamics correlate with extrinsic environmental and management drivers. One promising technique as a front-line detection method is environmental DNA (eDNA), which identifies genetic material discharged in the environment (water or sediment) by macro and microorganisms. This technique has great sensitivity and it can be used even when there is no visible presence of the target organism during sampling. Through the association of eDNA with farm environmental parameters it is possible to predict fish mortalities and advise the best approaches for disease management before outbreaks occur.

Ciliate protozoans are considered economically important parasites affecting many aquaculture species. Specifically, Chilodonella spp. are ciliates that can cause losses of 50−95% in fish stocks without early warnings. Chilodonella hexasticha was used as a model to investigate the potential use of environmental DNA (qPCR assay based on SSU-rDNA gene) and associated water quality data to predict protozoan parasite outbreaks in a freshwater barramundi farm from Australia. Using eDNA methodology, we were able to detect the abundance of our target species in as little as 15 mL of water collected from ponds within a commercial barramundi farm, over 10 months.  Increased C. hexasticha eDNA levels were found to be highly correlated with occurrence of later fish mortality events (r = 0.402; P < 0.001) and also with size of fish (r = - 0.189; P < 0.05). Furthermore, there were significantly more fish mortalities observed during the warmer, wetter monsoonal season compared to the cooler, dry season (1280 vs. 135 mortalities, respectively; P < 0.05).

This study shows that the incorporation of eDNA for parasite surveillance associated with local environmental data can predict disease outbreaks, allowing fish farmers to adopt preventive strategies to boost fish production (e.g. water treatment, improvement of oxygen levels, stock of juveniles in ponds after rainy season, etc.) and avoid economic losses.