Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

Abstract

In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples.DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and

Monitoring Non-indigenous Species in Port Habitats: First Application of a Standardized North American Protocol in the Mediterranean Sea

“…While this methodology provides a reliable option for sampling and monitoring fouling communities in the Mediterranean area, further analyses to test its effectiveness should be encouraged in other regional localities, together with a comparison to other fouling monitoring tools, including the use of genetic approaches (e.g., Ardura and Planes, 2017;Borrell et al, 2017;Marraffini et al, 2017;Cahill et al, 2018;Kakkonen et al, 2019;Obst et al, 2020Duarte et al, 2021. Similarly successful implementation in other locales could lead to the proposal of this method as an adopted standard for the assessment of marine bioinvasions in the Mediterranean.…”

“…During the last few years, the metabarcoding approach has also started to be employed in NIS surveys with satisfying results (see also Borrell et al, 2017;Miralles et al, 2021;Pearman et al, 2021). Metabarcoding can be considered as an efficient tool to detect cryptic species or early life stages, but one of the main disadvantages is the incompleteness of genetic sequence reference libraries (Zaiko et al, 2018;Duarte et al, 2021). For this reason, an integrative approach should be considered as the gold standard (Padial et al, 2010;Cahill et al, 2018;Obst et al, 2020;Duarte et al, 2021).…”

“…Metabarcoding can be considered as an efficient tool to detect cryptic species or early life stages, but one of the main disadvantages is the incompleteness of genetic sequence reference libraries (Zaiko et al, 2018;Duarte et al, 2021). For this reason, an integrative approach should be considered as the gold standard (Padial et al, 2010;Cahill et al, 2018;Obst et al, 2020;Duarte et al, 2021).…”

Revision and annotation of DNA barcode records for marine invertebrates: report of the 8thiBOL conference hackathon

“…The case for reviewing barcode data for marine invertebrates is particularly relevant. Marine invertebrates are often studied as a community and are one of the customary targets for marine biomonitoring, through metabarcoding (Duarte et al 2021). The reference libraries are still far from complete and just beginning for some groups (McGee et al 2019, Weigand et al 2019, Leite et al 2020 or geographical regions.…”

Managing human mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

“…Studies have demonstrated that the amplification of DNA barcode regions from eDNA (i.e. eDNA metabarcoding) can be used to detect marine NNS [32][33][34][35] and that it is a sensitive and accurate method for biomonitoring [36,37]. However, eDNA surveys are rarely used in conjunction with existing methods to detect NNS range shifts, and eDNA metabarcoding can validate, endorse, or highlight flaws, in current biodiversity management strategies.…”