ArticleMolecular ecology2021
Biases in bulk: DNA metabarcoding of marine communities and the methodology involved.
Article in Molecular ecology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
70 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Systematic Review: Long-Read Sequencing in Algal Studies.International journal of molecular sciences · 2026Pooled it
- Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review.Parasites & vectors · 2024Pooled it
- Getting to the Core of the Matter-Assessing the Role of Replication in Metabarcoding-Based sedaDNA.Molecular ecology resources · 2026Article
- A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.Molecular ecology resources · 2026Review
- Comparing Aquatic Environmental DNA, Microscopy and Sedimentary DNA to Investigate Cyanobacterial Community Dynamics Across a Trophic Gradient.Microbial ecology · 2026Article
- Article
- DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.Molecular ecology resources · 2026Article
- Phloxine B Staining is Compatible With High-Throughput DNA Barcoding of Meiofauna.Ecology and evolution · 2026Article
- Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.Molecular ecology resources · 2026Article
- Limitations of Common Molecular Markers in Fungal Biodiversity Analysis and the Benefits of Their Synergistic Use.Molecular ecology resources · 2026Article
- Phytoplankton Diversity in the Northern Adriatic Sea: Insights and Inconsistencies from Microscopy and Metabarcoding.Biology · 2026Article
- High-Throughput DNA Sequencing Reveals Gastric Content Composition and Inter-Specific Variation inEcology and evolution · 2026Article
- From fish to invertebrates: multi-marker eDNA metabarcoding for monitoring wetland biodiversity and non-indigenous species in Macao SAR China.Scientific reports · 2026Article
- Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.Molecular ecology resources · 2026Article
- Reactive oxygen species trigger downward vertical migration in diatom microphytobenthic biofilms as a strategy to cope with oxidative stress.The ISME journal · 2026Article
- The Evolution of Bees: Insights from 'Omic Studies.Genome biology and evolution · 2026Review
- Advances in the detection of antimicrobial resistance in aquatic environments: a methodological perspective.Biology methods & protocols · 2026Review
- Article
- Comparative metabarcoding study performed on the mock soil nematode communities, composed of DESS-preserved and freshly extracted nematodes.Journal of nematology · 2026Article
- Metabarcoding and targeted barcoding can enhance Norwegian Continental Shelf macrofauna species inventories.PeerJ · 2026Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly being implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, preprocessing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of three PCR replicates, and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, if appropriate controls are included along the data generation process, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.