eDNA and water quality tests to pre-empt disease outbreaks

Research out of Hong Kong which combines environmental DNA testing with water quality monitoring is showing promise as a method to predict risk of disease in aquaculture operations.

by Helen Taylor

The challenge

Disease prevention is a common struggle among fish and shrimp farmers worldwide. It has been estimated that diseases are responsible for up to 40% of production losses (depending on species and system), valued at more than USD100 billion per year. The challenge, says Giana, is that by the time fish are showing signs of disease, it is usually too late to save them and the stock is lost. Also, many of the chemicals used to treat disease outbreaks are detrimental to the animals and to the environment. So, a tool that could reliably predict the risk of a disease outbreak in time to prevent it would be invaluable.

At the freshwater pond station of Hong Kong government (Au Tau), monitoring installations deliver real-time data to In-Situ’s data services platform, HydroVu, for the team to download for analysis at anytime from anywhere.

The solution

This project, which is a continuation of research she began in Australia, is the first instance in which eDNA analysis, often factored into ecological studies, is being used in aquaculture to quantify pathogen abundance in water. It is also one of the first times, eDNA data is being used in conjunction with water quality data to provide information on both water-borne parasites and water quality parameters and how they are connected, and to give us clues to disease risks.

“A strong R&D focus on early identification of disease risk within aquaculture farms using environmental eDNA techniques and water quality monitoring (environmental sensing) associated with microbiome investigation can be used to solve one of the biggest challenges the aquaculture industry faces - outbreaks,” Giana says. She is adopting IoT, AI and molecular techniques as innovative ways to predict and manage disease risk in aquaculture.

The method

Giana is sampling in both open pen (marine) and pond (fresh water) operations. Every week a research assistant collects water from the sites and brings it to the laboratory to analyze the genetic information it carries.

In the meantime, monitoring installations that include In-Situ’s Aqua TROLL 500 Multiparameter Sondes and HydroMace data loggers, as well as rain gauges, deliver real-time data to In-Situ’s data services platform, HydroVu. The Aqua TROLL 500 is a fully customizable multiprobe with interchangeable sensors, automated antifouling wiper and smartphone interface designed to deliver accurate water quality data and simplified calibration. Built to withstand harsh environments, Aqua TROLL 500 is commonly used for both spot sampling and long-term, low-maintenance deployment in both fresh water and saltwater. Data transmission via telemetry to HydroVu gives Giana instant access to her data.

Giana’s team can download it for analysis at anytime from anywhere. The online app provided with the system helps both farmers and the team to monitor, in real time, the changes in water parameters. This is particularly important because in warm water aquaculture, water quality and production data collection and recording keeping are not as common as they are in the salmon industry.

Collecting continuous data on temperature, salinity, DO, pH, turbidity and rain measurement gives Giana the information she needs to correlate water quality and pathogen DNA abundance in water to find connections which can pre-empt disease outbreaks. Additionally, she is able to alert her participating farmers if there is a significant change in their water parameters and what measures to implement to avoid losses. Her current project idea originated from her PhD work based on eDNA and has been published elsewhere (https://www.sciencedirect.com/science/ article/pii/S0044848617307615?via%3Dihub).

Giana’s study was one of first to show the association between ciliate protozoan abundance in water and environmental parameters as a way to predict outbreaks. In the same study, she demonstrated that environmental DNA and qPCR could be used to determine the probability of mortalities in fish farms.

Reliable water quality monitoring equipment has been key to her project progress, says Giana. “With this equipment, I can trust that data is always being collected. The cost comparison was favorable, especially given the amount of data we’re getting; the installation was straightforward; and the company representatives were very helpful in getting everything set up.”

“If we can measure, we can predict. Then we can be proactive. ” - Dr Giana Bastos Gomes

The determination

Giana has been collecting data since late 2019 and will continue the project through the summer months in Hong Kong, because weather is an important contributing factor to water quality conditions in farms. Despite disruptions caused by the protests in Hong Kong and consequently, Covid-19, she is determined to complete the project and develop a model that will give farmers the assistance they need to predict disease risk in their stocks.

“I’d like to create an app that could predict disease risk,” she says. “There’s so much uncertainty in the industry because there is no data. The ability to use information to lower risk could benefit the farmers, investors, insurance companies and government policy teams.”

As the fastest growing agribusiness in the world, aquaculture has the potential to provide a critical food source for a growing population, with fewer environmental impacts than traditional agriculture.

“If we can measure, we can predict,” says Giana. “Then we can be proactive. Even a small improvement in mortality numbers can make a big difference to farmers.”

Helen Taylor, is Content Manager at In-Situ Inc. USA. Email: htaylor@in-situ.com