2013
DOI: 10.1186/1742-9994-10-45
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Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

Abstract: IntroductionInvertebrate communities are central to many environmental monitoring programs. In freshwater ecosystems, aquatic macroinvertebrates are collected, identified and then used to infer ecosystem condition. Yet the key step of species identification is often not taken, as it requires a high level of taxonomic expertise, which is lacking in most organizations, or species cannot be identified as they are morphologically cryptic or represent little known groups. Identifying species using DNA sequences can… Show more

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Cited by 208 publications
(239 citation statements)
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References 70 publications
(101 reference statements)
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“…Thus, studies on marine benthic communities that prove the suitability of DNA-based approaches for environmental biomonitoring are lacking. Using samples of known taxonomic composition, we show that an alternative barcode that targets a shorter region of the COI gene outperforms the 658 bp region that is commonly used for metabarcoding metazoans (Carew et al, 2013;Ji et al, 2013;Dowle et al, 2015;Elbrecht and Leese, 2015;Zaiko et al, 2015). Our data corroborate previous studies unveiling the lack of universality in the COI primers, which is translated to biases during PCR step (Pochon et al, 2013;Deagle et al, 2014).…”
Section: Effect Of Pcr-based Analysis Biases On Taxonomic Inferencessupporting
confidence: 81%
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“…Thus, studies on marine benthic communities that prove the suitability of DNA-based approaches for environmental biomonitoring are lacking. Using samples of known taxonomic composition, we show that an alternative barcode that targets a shorter region of the COI gene outperforms the 658 bp region that is commonly used for metabarcoding metazoans (Carew et al, 2013;Ji et al, 2013;Dowle et al, 2015;Elbrecht and Leese, 2015;Zaiko et al, 2015). Our data corroborate previous studies unveiling the lack of universality in the COI primers, which is translated to biases during PCR step (Pochon et al, 2013;Deagle et al, 2014).…”
Section: Effect Of Pcr-based Analysis Biases On Taxonomic Inferencessupporting
confidence: 81%
“…Several studies analyzing the same samples with morphological and molecular taxonomy have been performed so far to benchmark COI based metabarcoding in animals, all focusing exclusively on freshwater or terrestrial macroinvertebrates Carew et al, 2013;Gibson et al, 2014;Dowle et al, 2015;Elbrecht and Leese, 2015) or carried out under morphological identifications limited to high taxonomic levels (Gibson et al, 2015). Thus, studies on marine benthic communities that prove the suitability of DNA-based approaches for environmental biomonitoring are lacking.…”
Section: Effect Of Pcr-based Analysis Biases On Taxonomic Inferencesmentioning
confidence: 99%
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“…Metabarcoding based on PCR cannot yet provide reliable biodiversity indices since, especially for eukaryotes, it does not supply information on the abundance of every single species detected (Lindeque et al, 2013;Hirai et al, 2015). Most of the studies aimed at evaluating the relationships between species abundance and metabarcoding data obtained looser associations (Carew et al, 2013;Zhou et al, 2013;Hirai et al, 2015). Conversely, stronger relationships have been reported between biomass and read proportions (Elbrecht and Leese, 2015).…”
Section: Use Of Metabarcoding To Study Marine Biodiversitymentioning
confidence: 97%
“…During recent years, DNA metabarcoding of whole communities has become a new powerful tool for environmental monitoring of aquatic ecosystems (Hajibabaei et al 2011, Carew et al 2013, Elbrecht and Leese 2015, Gibson et al 2015. The DNA-based assays to monitor species biodiversity proved to be a rapid and efficient tool that allows the recovery of a substantial amount of taxa (Sweeney et al 2011, Taberlet et al 2012, Yu et al 2012, Carew et al 2013.…”
Section: Introductionmentioning
confidence: 99%