Absolute quantification of priority bacteria in aquaculture using digital PCR

Area of Science:

• Aquatic microbiology
• Molecular diagnostics
• Fish health management

Background:

• Aquaculture systems require high water quality for fish health and production.
• Microorganisms impact nutrient cycling, hydrogen sulfide (H₂S) production, and fish health.
• Current bacterial monitoring methods lack precision, specificity, and sensitivity.

Purpose of the Study:

• To demonstrate Digital PCR as a powerful tool for absolute quantification of key bacteria in aquaculture.
• To develop ultra-sensitive assays for sulfate-reducing bacteria (SRB) and major fish pathogens.
• To assess assays for human pathogens relevant to salmonid cultivation and processing.

Main Methods:

• Digital PCR (dPCR) for absolute quantification of bacterial DNA.
• Development of single-plex and multiplex assays using TaqMan® probe technology.
• Quantification of *Moritella viscosa*, *Yersinia ruckeri*, *Flavobacterium psychrophilum*, *Listeria monocytogenes*, and *Desulfovibrio desulfuricans*.

Main Results:

• Established an ultra-sensitive dPCR assay for SRB quantification.
• Achieved limits of detection as low as 2 fg DNA for *L. monocytogenes* and *D. desulfuricans*.
• Demonstrated dPCR's capability for simultaneous quantification of multiple aquaculture priority bacteria.

Conclusions:

• Digital PCR provides a precise and sensitive method for monitoring critical bacteria in aquaculture.
• This technology can enhance fish health management and prevent losses due to pathogens and H₂S.
• dPCR assays offer a significant improvement over traditional methods for aquaculture microbiology.