Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

Ji, Yinqiu; Ashton, Louise A.; Pedley, Scott M.; Edwards, David P.; Tang, Yong; Nakamura, Akihiro; Kitching, R. L.; Dolman, Paul M.; Woodcock, Paul; Edwards, Felicity A.; Larsen, Trond H.; Hsu, Wayne W.; Benedick, Suzan; Hamer, Keith C.; Wilcove, David S.; Bruce, Catharine; Wang, Xiaoyang; Levi, Taal; Lott, Martin; Emerson, Brent C.; Yu, Douglas W.

doi:10.1111/ele.12162

Cited by 558 publications

(619 citation statements)

References 76 publications

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“…Moreover, barcoding has increased for rapid biodiversity assessment and biomonitoring for many terrestrial taxa (Yu et al 2012, Taberlet et al 2012, Brehm et al 2013. Ji et al (2013) compared metabarcoded samples of arthropods and birds with standard biodiversity data sets, and found that the genetic data sets were taxonomically more comprehensive, quicker to produce and less reliant on taxonomic expertise. Cristescu (2014) raised the urge for a coordinated progression of species barcoding that integrates taxonomic expertise and genetic data.…”

Section: Using Metabarcoding Data For Chironomid Diversity Assessmentmentioning

confidence: 99%

Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands

Theissinger¹,

Kästel²,

Elbrecht³

et al. 2017

Metabarcoding and Metagenomics

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The biocide Bacillus thuringiensis var. israelensis (Bti) is widely applied for mosquito control in temporary wetlands of the German Upper Rhine Valley. Even though Bti is considered environmentally friendly, several studies have shown non-target effects on chironomids, a key food resource in wetland ecosystems. Chironomids have been proposed as important indicators for monitoring freshwater ecosystems, however, morphological determination is very challenging. In this study, we investigated the effectiveness of metabarcoding for chironomid diversity assessment and tested the retrieved chironomid operational taxonomic units (OTUs) for possible changes in relative abundance and species diversity in relation to mosquito control actions in four temporary wetlands. Three of these wetlands were, for the first year after 20 years of Bti treatment, partly left Bti-untreated in a split field design, and one wetland has never been treated with Bti. Our metabarcoding approach detected 54 chironomid OTUs across all study sites, of which almost 70% could be identified to species level comparisons against the BOLD database. We showed that metabarcoding increased chironomid species determination by 70%. However, we found only minor significant effects of Bti on the chironomid community composition, even though Bti reduced chironomid emergence by 65%. This could be due to a time lag of chironomid recolonization, since the study year was the first year of Bti intermittence after about 20 years of Bti application in the study area. Subsequent studies will have to address if and how the chironomid community composition will recover further in the now Bti-untreated temporary wetlands to assess effects of Bti.

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Section: Using Metabarcoding Data For Chironomid Diversity Assessmentmentioning

confidence: 99%

Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands

Theissinger¹,

Kästel²,

Elbrecht³

et al. 2017

Metabarcoding and Metagenomics

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“…Thus instead of identifying one species from a single water sample, an eDNA metabarcoding approach has the potential to identify the eDNA of any taxon collected in a water sample given that the DNA sequences are already deposited in a repository. Thus, metabarcoding can be used as a tool to produce biodiversity estimates that are taxonomically comprehensive, quicker to produce, and less reliant on taxonomic expertise (Ji et al, 2013). 5.…”

Section: Edna Applications In Ecology and Conservationmentioning

confidence: 99%

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Díaz-Ferguson

Moyer

2014

RBT

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Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.Key words: environmental DNA (eDNA), detection probability, occupancy models, persistence, metabarcode, minibarcode.In order to understand distributions, patterns, and abundances for populations or species, the collection (detection) and identification of individuals from their physical origins must be undertaken. Thus, species detection is fundamental to scientific disciplines such as phylogenetics, conservation biology, and ecology. However, species detection is sometimes extremely difficult especially in marine and aquatic environments where organisms have complex life cycles, and direct observation of early development stages is almost impossible (Ficetola, Miaud, Pompanon, & Taberlet, 2008). Species detection in these environments has been conducted using traditional direct observation methods (visual or acoustic) (Thomsen et al., 2012a). Nonetheless, traditional detection methods can have logistic limitations, be time consuming, expensive, and in some cases, harmful to the environment (e.g., marine bottom trawls, electrofishing and rotenone poisoning) (Thomsen et al., 2012b). The advent of novel molecular and forensic methods have provided innovative tools for detecting marine and aquatic organisms that may circumvent the aforementioned limitations (Darling & Blum, 2007;valentini, Pompano, & Taberlet, 2009;Lodge et al., 2012).One such tool is the detection of an organism's environmental DNA (eDNA). Defined as short DNA fragments that an organism leaves behind in non-living components of the ecosystem (i.e., water, air or sediments), eDNA is derived from either cellular DNA present in epithelial cells released by organisms to the environment through skin, urine, feces or mucus or extracellular DNA that is the DNA in the environment resulting from cell death and subsequent destruction of cell structure (Foote, Thomsen, Sveegaard, Wahlberg, Kielgast, Kyhn, Salling, Galatius, Orlando, & Gilbert, 2012;Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012a). Methodologically, eDNA d...

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“…Recent research has begun to validate metabarcoding as a time and cost‐efficient method for biodiversity surveys in terrestrial, freshwater, and marine ecosystems (Hirai, Kuriyama, Ichikawa, Hidaka, & Tsuda, 2015; Ji et al., 2013; Thomsen et al., 2012; Valentini et al., 2016). The results of metabarcoding studies depend on the markers used providing sufficient taxonomic coverage and resolution for the taxa of interest.…”

Section: Introductionmentioning

confidence: 99%

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

Clarke

Beard

Swadling

et al. 2017

Ecology and Evolution

169

193

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DNA metabarcoding is a promising approach for rapidly surveying biodiversity and is likely to become an important tool for measuring ecosystem responses to environmental change. Metabarcoding markers need sufficient taxonomic coverage to detect groups of interest, sufficient sequence divergence to resolve species, and will ideally indicate relative abundance of taxa present. We characterized zooplankton assemblages with three different metabarcoding markers (nuclear 18S rDNA, mitochondrial COI, and mitochondrial 16S rDNA) to compare their performance in terms of taxonomic coverage, taxonomic resolution, and correspondence between morphology‐ and DNA‐based identification. COI amplicons sequenced on separate runs showed that operational taxonomic units representing >0.1% of reads per sample were highly reproducible, although slightly more taxa were detected using a lower annealing temperature. Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across zooplankton phyla. However, mitochondrial COI resolved up to threefold more taxa to species compared to 18S. All markers revealed similar patterns of beta‐diversity, although different taxa were identified as the greatest contributors to these patterns for 18S. For calanoid copepod families, all markers displayed a positive relationship between biomass and sequence reads, although the relationship was typically strongest for 18S. The use of COI for metabarcoding has been questioned due to lack of conserved primer‐binding sites. However, our results show the taxonomic coverage and resolution provided by degenerate COI primers, combined with a comparatively well‐developed reference sequence database, make them valuable metabarcoding markers for biodiversity assessment.

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Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

Cited by 558 publications

References 76 publications

Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands

Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

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