4 | DISCUSSION
The aim of this study was to avail of a state-of-the-art technology (HT-qPCR) to facilitate the cost- and time-effective development and application of a molecular screening toolkit in a case study to detect a range of bivalve and decapod larvae in zooplankton samples. The overall process was divided into three main phases consisting of the definition of target taxa and establishment of reference databases (PHASE 1);in silico selection and in vitro assessment of molecular assays (PHASE 2); and field testing and validation (PHASE 3). While PHASE 1 is communal to any general protocol aiming at developing taxon-specific molecular assays, PHASE 2 and 3 are enabled by the HT-qPCR platform. Following initial marker selection, and in silico and in vitro assessment, the resulting panel of assays included a total of 42 marker/species combinations targeting 24 species of relevance to Irish coastal marine ecosystems and of interest to the local shellfish aquaculture industry. The molecular toolkit (indirect method) performed well when validated on actual zooplankton samples by comparison to a direct method (microscopy), which was used to determine presence and abundance of bivalve and decapod larvae. The following sections address considerations and resulting recommendations of this new approach, which shows great potential in boosting the development of biomonitoring and ecological assessment tools.