Early Alert of Biological Risk in a Coastal Lagoon Through eDNA Metabarcoding

Abstract

Mediterranean coastal lagoons are environmentally important ecosystems whose conservation has been challenged due to anthropogenic impacts that promoted the expansion of non-indigenous and, sometimes, invasive species. Therefore, it is crucial to inventory biodiversity in these areas for the development of strategies of conservation and management. Classical methods used for biodiversity surveys and detection of non-native species may be unsuccessful for the detection and identification of species in early development stages such as cryptic, microscopic, elusive, and new coming species at low population density. The development of metabarcoding techniques in the last decade offers new opportunities for reliable biodiversity surveillance and facilitates early detection of nuisance species. The objective of this study was to analyze the species occurring in the protected coastal lagoon Canet-Saint Nazaire using a simple sampling protocol based on water samples and environmental DNA (eDNA) metabarcoding with a single barcode (cytochrome c oxidase subunit I [COI] gene). Two invasive species (Polydora cornuta and Acartia tonsa), two polychaete bioindicators of pollution (Hediste diversicolor and Capitella capitata), and one alga that produces harmful algal blooms were detected from only 6 L of water, indicating environmental degradation in the lagoon despite its protected status. These results demonstrate the importance of COI as single barcode together with eDNA as an ecological early warning system and suggest the need for environmental restoration in this lagoon.

Metabarcoding as a tool to enhance marine surveillance of nonindigenous species in tropical harbors: A case study in Tahiti

“…The analysis of eDNA can be effectively used to complement existing biomonitoring techniques through metabarcoding of entire biological communities (e.g., Carvalho et al., 2019; de Vargas et al., 2015; Fonseca et al., 2010; Keeley et al., 2018; Pearman et al., 2019; Shi et al., 2011). Environmental DNA metabarcoding has been proposed as a future tool for early and cost‐effective screening for NIS (e.g., Brown et al., 2016; Chain et al., 2016; Chariton et al., 2010; Darling et al., 2017; Suarez‐Menendez et al., 2020; Wood et al., 2013) from a range of environmental samples to complement marine surveillance programs. Extensive research efforts using metabarcoding and other species‐specific real‐time quantitative assays have focused on understanding detection limits, improving sampling and analytical methods, and elucidating the distribution and fate of nucleic acids from a range of NIS in controlled and field settings (von Ammon et al., 2018a, 2018b, 2019; Pochon et al., 2013, 2017; Rey et al., 2020; Wood et al., 2020; Wood, et al., 2019a, 2019b; Zaiko et al., 2016; Zhan et al., 2013).…”

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

“…After careful inspection we found 34 papers that indeed employed metabarcoding for NIS surveillance in marine and coastal ecosystems and that were retained to perform our analysis. We found 8 additional papers, in our personal collections, that were not displayed during our search, but that have relevant information and, therefore, were included in the analysis (Chain et al 2016, Ardura et al 2017, Koziol et al 2018, Leduc et al 2019, Suarez-Menendez et al 2020 (Table S2).…”

“…1B) (e.g. Borrell et al 2017, Rey et al 2019, Suarez-Menendez et al 2020 or to zooplankton (e.g. Zaiko et al 2015a,b, Abad et al 2016, Darling et al 2018, Lin et al 2020.…”

“…One possibility to increase the throughput volume of capture filters and reduce filtration time may be provided by the use of pre-filters with a larger pore size, followed by a second filtration of a smaller volume through a smaller pore (Ardura et al 2015 (Table S3). Filtering small volumes through independent filters, to avoid filter clogging, and pooling results together during sequence analysis, can be another valid option (Leduc et al 2019, Suarez-Menendez et al 2020.…”

“…The depth at which the water is sampled is another technical aspect that varied across studies (Table S3). Most studies sampled surface water (10-30 cm) (Borrell et al 2017, Koziol et al 2018, Holman et al 2019, Huhn et al 2020, Suarez-Menendez et al 2020), but many others sampled different depths to increase representativeness (Lacoursière-Roussel 2018, Leduc et al 2019, Rey et al 2020, Westfall et al 2020. Vertical eDNA distribution in the water column may vary as a function of several factors (e.g.…”