loading page

Development and validation of a DNA-based multi-species biomonitoring toolkit using a High-Throughput qPCR platform: a case study of Irish shellfish species
  • +1
  • Dennis van der Pouw Kraan,
  • Conor Graham,
  • Fiona Kavanagh,
  • Luca Mirimin
Dennis van der Pouw Kraan
Atlantic Technological University - Galway City

Corresponding Author:[email protected]

Author Profile
Conor Graham
Atlantic Technological University - Galway City
Author Profile
Fiona Kavanagh
Atlantic Technological University - Galway City
Author Profile
Luca Mirimin
Atlantic Technological University - Galway City
Author Profile


Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious conventional techniques (e.g. direct capture) and greater taxonomic resolution especially in complex life cycles and early life stages. However, tradeoffs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled High Throughput quantitative PCR platform (HT-qPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 24 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of target taxa and establishment of reference databases (PHASE 1); in silico selection/development and in vitro assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). Of a total of 85 assays in silico, 42 were eventually chosen and validated in vitro. Genetic signal showed good correlation with direct visual counts by microscopy, but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the development and application of panels of molecular assays for the monitoring and management of natural resources that can be applied to a range of monitoring programmes. Keywords: DNA, High Throughput, qPCR, biomonitoring, shellfish
11 Jul 2023Submitted to Molecular Ecology Resources
19 Jul 2023Submission Checks Completed
19 Jul 2023Assigned to Editor
19 Jul 2023Review(s) Completed, Editorial Evaluation Pending
04 Aug 2023Reviewer(s) Assigned
07 Nov 2023Editorial Decision: Revise Minor
24 Jan 20242nd Revision Received
24 Jan 2024Submission Checks Completed
24 Jan 2024Assigned to Editor
24 Jan 2024Review(s) Completed, Editorial Evaluation Pending
25 Jan 2024Editorial Decision: Accept