Pest Alert Tool—a web-based application for flagging species of concern in metabarcoding datasets

Abstract

Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitoring. Moreover, even non-scientists can now collect an eDNA sample, send it to a specialized laboratory for analysis and receive in-depth biodiversity record from a sampling site. This offers unprecedented opportunities for biodiversity assessments across wide temporal and spatial scales. The large volume of data produced by metabarcoding also enables incidental detection of species of concern, including non-indigenous and pathogenic organisms. We introduce an online app—Pest Alert Tool—for screening nuclear small subunit 18S ribosomal RNA and mitochondrial cytochrome oxidase subunit I datasets for marine non-indigenous species as well as unwanted and notifiable marine organisms in New Zealand. The output can be filtered by minimum length of the query sequence and identity match. For putative matches, a phylogenetic tree can be generated through the National Center for Biotechnology Information’s BLAST Tree View tool, allowing for additional verification of the species of concern detection. The Pest Alert Tool is publicly available at https://pest-alert-tool-prod.azurewebsites.net/.

Marine Non-Indigenous Species Dynamics in Time and Space within the Coastal Waters of the Republic of Ireland

“…An increasing number of modern technologies and approaches are used in monitoring marine life, including optoacoustic, omics, satellites, remote sensors, and artificial intelligence [31,32]. In the context of unwanted and non-indigenous species, DNA-based approaches have shown great promise thanks to the possibility to detect species' presence using indirect methods such as environmental DNA (eDNA) [33,34]. This is particularly useful in marine environments, where areas to be surveyed can be large and inaccessible, and taxonomic resolution can be hampered either by indistinguishable early life stages or by lack of taxonomic expertise.…”

“…Such approaches can also be extremely cost-effective when combined with more traditional survey methods by covering larger areas and helping focus resources on the greatest area of need, i.e., highest risk areas. While presence of a NIS can only be ascertained by direct capture and characterisation (using morphologic and/or genetic data), integrated eDNA data can be obtained at faster and wider temporal and spatial scales (e.g., citizen science approach) (e.g., [39]), with emerging web-based tools aiding the fast screening of large eDNA-based datasets (e.g., [34]). The possibility to detect new introductions at their first entry is important for the identification and effective management of pathways and vectors, thus eDNA is likely to become a key component of future NIS surveillance programmes.…”

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

“… 2 Metabarcoding datasets can be automatically screened for quick flagging of species of concern. 43 Faster and more accurate data collection increase our ability for early NIS detection and ultimately improves biodiversity management.…”