Résumé
High-throughput sequencing (HTS) technologies offer new promise to support
surveillance programs targeting marine non-indigenous species (NIS).
Metabarcoding might surpass traditional monitoring methods, for example
through its ability to detect rare species, a key feature in early
detection of NIS. Another interest of this approach is the identification
of organisms difficult to identify based on morphology only (e.g., early
developmental stages), making it relevant in the context of management
programs. Because many marine benthic NIS have a bi-phasic bentho-pelagic
life cycle, targeting their pelagic larval stages in zooplankton may allow
early detection and assessment of their establishment and potential
spread. We illustrate this approach with an analysis of bulk-DNA retrieved
from a time-series of zooplankton samples collected over 22 months in one
bay in Brittany (France). Using HTS of amplicons obtained with two markers
(COI and 18S) and a metabarcoding approach, 12 NIS were identified and
their temporal larval dynamics were monitored. Importantly, we chose to
focus on a closed list of species, from four metazoan classes encompassing
52 NIS reported within the study area or nearby seas, with molecular
references available or obtained locally for 42 of them. The use of a
custom-designed database allowed the detection of three NIS otherwise not
detected when using public databases. Interestingly, NIS known to have a
short-lived larval stage were detected (e.g., the bryozoan Bugula neritina
or the tunicate Corella eumyota). For two molluscs Ruditapes philippinarum
and Crepidula fornicata, metabarcoding results were compared to those
obtained using traditional methods (i.e., barcoding of individual larvae
and morphology, respectively) to show the reliability of the approach in
detecting and assessing the extent of their reproductive periods. Our
results also revealed that the Pacific oyster Crassostrea gigas, a
notorious invasive species, failed to reproduce in the study bay, showing
that metabarcoding on larval stages also provides information regarding
the establishment success (or failure) of NIS. While metabarcoding has its
limitations and biases, this study demonstrates its effectiveness for
surveillance of targeted NIS, notably to support management strategies
like the European Marine Strategy Framework Directive (MSFD).