Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

“…An increasing number of studies are using metabarcoding to characterize species diversity, or to detect rare or invasive species in environmental samples (Aylagas, Borja, Irigoien, & Rodríguez‐Ezpeleta, ; Brown, Chain, Zhan, MacIsaac, & Cristescu, ; de Vargas et al, ; Pochon, Zaiko, Fletcher, Laroche, & Wood, ; Zaiko et al, ). Unlike targeted approaches, metabarcoding enables many species to be identified simultaneously, and dependent on the approaches used, the taxa may represent multiple trophic levels (Keeley, Wood, & Pochon, ). However, many studies have highlighted challenges related to the amplification of multi‐template sequences (Zinger et al, ) including: primers that are not truly universal, primer biases (Clarke, Soubrier, Weyrich, & Cooper, ; Deagle, Jarman, Coissac, Pompanon, & Taberlet, ), “tag jumps”, which occur when the tag assigned to one particular sample is recombined to sequences belonging to another sample (Taberlet, Bonin, Zinger, & Coissac, ), different results based on choice of bioinformatic pipelines (von Ammon et al, ), and incomplete or inaccurate reference databases resulting in misassignment of taxa (Dowle et al, ; Nilsson et al, ; Wangensteen, Palacín, Guardiola, & Turon, ).…”

Linking Environmental DNA and RNA for Improved Detection of the Marine Invasive Fanworm Sabella spallanzanii

“…A suite of different molecular techniques have been applied for analyzing eDNA/eRNA in marine samples which allow for either single species detection or community-wide taxonomic characterization (Wood et al, 2013). For the latter, metabarcoding has predominantly been used to characterize biodiversity and explore community/functional shifts in response to natural or anthropogenic perturbations (Langlet et al, 2013;Aylagas et al, 2014Aylagas et al, , 2018Pawlowski et al, 2016;Keeley et al, 2018;Laroche et al, 2018;Stoeck et al, 2018). Metabarcoding utilizes universal primers that target taxonomically informative genes such as, the nuclear small subunit ribosomal RNA (18S rRNA) or the mitochondrial Cytochrome c Oxidase subunit I (COI) genes (Tanabe et al, 2016;Stat et al, 2017;Bista et al, 2018;Wangensteen et al, 2018).…”

Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm (Sabella spallanzanii) and club tunicate (Styela clava)

“…In aquatic systems, these techniques rely on collecting and detecting either (i) entire organisms (particularly in the case of microorganism such as bacteria, microalgae, zooplankton), (ii) cells of organisms that may originate from various sources, including scales, faeces, epidermal mucus, urine, saliva, and gametes (Barnes et al 2014), or (iii) extracellular DNA that can be free-floating or particle-bound. These techniques have been applied to determine aquatic biodiversity or the presence (and in some cases abundance) of specific taxa in a wide range of habitats (e.g., Thomsen et al 2012b;Dowle et al 2016;Laroche et al 2016;Ulibarri et al 2017;Keeley et al 2018). Studies have shown that in some situations molecular methods can be more efficient for detecting species than traditional approaches (Dejean et al 2012;Keskin 2014;Zaiko et al 2016), making them a promising tool for the early detection of newly introduced species and for monitoring the dispersal of established taxa (Blanchet 2012;Piaggio et al 2014;Rees et al 2014;Comtet et al 2015).…”