Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

By A. Valentini, P. Taberlet, C. Miaud, Raphaël Civade, Jelger E. Herder, P. F. Thomsen, E. Bellemain, Aurélien Besnard, É. Coissac, Frédéric Boyer and 17 more. Molecular Ecology, 2016

1,184 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/79b162a83cf3274e9de57f9c8b2606b3ac0df018

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Citations in the corpus

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, methodology): “Another option that could be used involves selection of a threshold based on availability of empirical data as was performed in Valentini et al. (2016).”
Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA (2020, background): “…eDNA in water samples (Goldberg, Strickler, & Fremier, 2018; Ishige et al., 2017; Minamoto et al., 2012; Miya et al., 2015; Ushio et al., 2018; Valentini et al., 2016); however, several recent studies have targeted eDNA in underwater sediments (Buxton, Groombridge, & Griffiths, 2018; Shaw et…”
Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods (2018, methodology): “64 While these studies detected known target species using specific PCR primers, recent 65 advances in the technology of metabarcoding using universal PCR primers enabled us to 66 elucidate the complete biodiversity using eDNA (Thomsen et al., 2012a; Kelly et al., 2014a; 67 Valentini et al., 2016).”
Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness (2020, background): “The number of sites across studies was highly uneven – 56% of comparative observations originated from just three publications, all of which sampled freshwater systems (Valentini et al., 2016; Fujii et al., 2019; Li et al., 2019).”
GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding (2021, background): “…survey aquatic biodiversity, eDNA metabarcoding has recently emerged as a promising approach, frequently surpassing traditional inventory methods in detectability potential (Boussarie et al., 2018; Carraro, Hartikainen, Jokela, Bertuzzo, & Rinaldo, 2018; Stat et al., 2019; Valentini et al., 2016).”
eDNA Sampler: A fully integrated environmental DNA sampling system (2018, background): “…includes terrestrial animal detection from water samples (Williams, Huyvaert, Vercauteren, Davis, & Piaggio, 2018), in addition to biodiversity assessment via eDNA metabarcoding methods (Valentini et al., 2016). eDNA sampling methods, however, are still under development (Goldberg et al., 2016).”
DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, background): “Sequencing of environmental samples such as seawater is now applied in a macrobial sense across a range of trophic levels (“microbes to mammals”) (Trivedi et al., 2016; Valentini et al., 2016), and approaches used to inventory individuals (Ardura et al.”
Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, methodology): “Various regions of 12S have been proposed as metabarcoding markers, including a ca. 63 bp fragment (Valentini et al., 2016), a ca. 106 bp fragment (Kelly et al., 2014a; Riaz et al., 2011), and a ca. 171 bp fragment (Miya et al., 2015).”
Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea (2019, methodology): “…Wilcox et al., 2013; Sigsgaard et al., 2015) and 2) multispecies detection by NextGeneration Sequencing (NGS) after PCR amplification of eDNA using universal primers that target short mitochondrial DNA barcoding regions – eDNA metabarcoding (e.g. Valentini et al., 2015; Sigsgaard et al., 2016).”
Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes (2020, methodology): “We followed a strict contamination control protocol in both field and laboratory stages (Goldberg et al., 2016; Valentini et al., 2016).”
Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter (2017, methodology): “Aqueous eDNA is an emerging increasingly sensitive technique for revealing species distributions (e.g. Jane et al. 2015; Valentini et al. 2016), early detection of invasive species (e.g. Smart et al. 2015; Simmons et al. 2016) and monitoring rare and/or threatened species for conservation (e.g.…”
Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment (2018, methodology): “There is probably persisting free-floating eDNA (extracellular DNA) which could also influence the results of the metabarcoding approach. eDNA is a promising area often used to detect rare, endangered or invasive species in aquatic ecosystems (e.g., Valentini et al., 2016).”
Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment (2016, background): “…is increasingly applied to water (e.g., Ficetola et al., 2008; Foote et al., 2012; Thomsen et al., 2012; Kelly et al., 2014; Davy et al., 2015; Valentini et al., 2016), soil (Taberlet et al., 2012b), and sediment samples (Guardiola et al., 2015; Turner et al., 2015; Pearman et al., 2016).”