A non-lethal method for detection of Bonamia ostreae in flat oyster (Ostrea edulis) using environmental DNA

Abstract

Surveillance and diagnosis of parasitic Bonamia ostreae infections in flat oysters (Ostrea edulis) are prerequisites for protection and management of wild populations. In addition, reliable and non-lethal detection methods are required for selection of healthy brood oysters in aquaculture productions. Here we present a non-lethal diagnostic technique based on environmental DNA (eDNA) from water samples and demonstrate applications in laboratory trials. Forty oysters originating from Limfjorden, Denmark were kept in 30 ppt sea water in individual tanks. Water was sampled 6 days later, after which all oysters were euthanized and examined for infection, applying PCR. Four oysters (10%) were found to be infected with B. ostreae in gill and mantle tissue. eDNA purified from the water surrounding these oysters contained parasite DNA. A subsequent sampling from the field encompassed 20 oysters and 15 water samples from 5 different locations. Only one oyster turned out positive and all water samples proved negative for B. ostreae eDNA. With this new method B. ostreae may be detected by only sampling water from the environment of isolated oysters or isolated oyster populations. This non-lethal diagnostic eDNA method could have potential for future surveys and oyster breeding programs aiming at producing disease-free oysters.

Application of Environmental DNA for Monitoring Red Sea Bream Iridovirus at a Fish Farm

“…eDNA has been studied extensively since the 2000s with numerous applications, such as metagenomics, species detection, or biomass estimation ( 1 , 2 ). Aquatic animal pathogens are basically waterborne; therefore, eDNA has been studied as a potential tool for monitoring aquatic animal diseases in aquaculture ( 3 – 5 ) and border control ( 6 , 7 ). Although the term “eDNA” has not been used in fish virus research, eDNA could be applied in monitoring waterborne viruses in combination with virus concentration techniques.…”

Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data

“…Here, we have demonstrated that eDNA barcoding can be employed to characterize the species composition of captured fish from the meltwater leftover in industrial and artisanal fishing operations. eDNA is gaining popularity and utility in fisheries and seafood research and has the potential to be a potent and complementary tool to the growing number of approaches to improving traceability throughout the seafood supply chain [ 38 , 40 , 54 , 55 ]. Built upon nearly two decades of studies applying the well-vetted concept of DNA barcoding to identify fish to species level [ 16 , 56 ], the eDNA approach is positioned to be both a familiar and a transformative tool in improving seafood monitoring.…”

Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review

“…In the case of single species detection, eDNA is subjected to amplification with species-specific primer [ 44 ]. Here, conventional PCR (cPCR) can be used to conduct a ‘presence and absence’ study whereas quantitative PCR (qPCR) is more preferred for quantification of targeted DNA and elimination of false positive or negative results [ 16 , 45 ].…”

“…Recently, CRISPR-Cas is gaining popularity in eDNA-based species detection [ 46 ]. Moreover, in all cases, positive and negative controls should be maintained [ 44 ].…”

“…In the field, contamination is a major issue for inter and intra sampling. The sterilized sampling boots or sterile chest waders should be used when the researcher is required to reach deep into the sampling site for sample collection [ 44 ]. It is highly recommended that all tools should be sterilized with 10–50% bleach solution followed by deionized water (>2 times) [ 30 ].…”