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.