ArticlePloS one2019
COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Desiccation to DNA: Bulk DNA Metabarcoding of Macroinvertebrate Egg Banks via Sugar-Flotation Enhances Biodiversity Surveys of Dry Salt Lakes.Ecology and evolution · 2026Article
- Understanding biological control function and trophic interaction dynamics of an artificially released predatory bug by DNA metabarcoding.Insect science · 2026Article
- Fine-Scale Ecological Biomonitoring in a Large, Complex Agriculturally Impacted Watershed via eDNA Metabarcoding.Molecular ecology · 2026Article
- Accuracy of occurrence and abundance estimates from insect metabarcoding.bioRxiv : the preprint server for biology · 2026Article
- From fish to invertebrates: multi-marker eDNA metabarcoding for monitoring wetland biodiversity and non-indigenous species in Macao SAR China.Scientific reports · 2026Article
- The shared performance of different COI regions increases the niche breadth detectable from bat guano eDNA.Genetics and molecular biology · 2026Article
- Annual dietary shifts of lumpfish (BMC marine science · 2026Article
- Soil communities following harvest have different early successional dynamics compared with post-wildfire patterns.Scientific reports · 2025Article
- Biomonitoring 2.0 Refined: observing local change through metaphylogeography using a community-based eDNA metabarcoding monitoring network.BMC biology · 2025Article
- Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.Molecular ecology resources · 2025Article
- Multi-method survey rediscovers critically endangered species and strengthens Madagascar's freshwater fish conservation.Scientific reports · 2024Article
- Three steps towards comparability and standardization among molecular methods for characterizing insect communities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton.Scientific reports · 2023Article
- Analysis of trapped mosquito excreta as a noninvasive method to reveal biodiversity and arbovirus circulation.Molecular ecology resources · 2023Article
- Article
- Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment.Scientific reports · 2022Article
- DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish.Molecular ecology · 2022Article
- Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.iScience · 2022Article
- Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods.GigaScience · 2022Article
- A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey.Molecular ecology resources · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mixed community or environmental DNA marker gene sequencing has become a commonly used technique for biodiversity analyses in freshwater systems. Many cytochrome c oxidase subunit I (COI) primer sets are now available for such work. The purpose of this study is to test whether COI primer choice affects the recovery of arthropod richness, beta diversity, and recovery of target assemblages in the benthos kick-net samples typically used in freshwater biomonitoring. We examine six commonly used COI primer sets on samples collected from six freshwater sites. Biodiversity analyses show that richness is sensitive to primer choice and the combined use of multiple COI amplicons recovers higher richness. Thus, to recover maximum richness, multiple primer sets should be used with COI metabarcoding. In ordination analyses based on community dissimilarity, samples consistently cluster by site regardless of amplicon choice or PCR replicate. Thus, for broadscale community analyses, overall beta diversity patterns are robust to COI marker choice. Recovery of traditional freshwater bioindicator assemblages such as Ephemeroptera, Trichoptera, Plectoptera, and Chironomidae as well as Arthropoda site indicators were differentially detected by each amplicon tested. This work will help future biodiversity and biomonitoring studies develop not just standardized, but optimized workflows that either maximize taxon-detection or the selection of amplicons for water quality or Arthropoda site indicators.
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