Scrutinizing key steps for reliable metabarcoding of environmental samples

By A. Alberdi, O. Aizpurua, M. Gilbert, Kristine Bohmann. 2018

553 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/cdcb6337f18e0c6c62126dbf14186f71121b1c70

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Citations in the corpus

Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, background): “Low quantities of template DNA and stochasticity in early PCR cycles is a known factor in causing poor reproducibility (Alberdi et al., 2018; Collins et al., 2018; Leray & Knowlton, 2017), and can be ameliorated by performing multiple PCR technical replicates (Ficetola et al.”
The Elephant in the Lab (and Field): Contamination in Aquatic Environmental DNA Studies (2020, background): “While these conservative approaches decrease the potential for false positives, they do increase false-negatives rates and may lead to incorrect inference about target species presence or diversity (Alberdi et al., 2018; Zinger et al., 2019).”
Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds (2020, methodology): “5 μl, bright band = 5 μl) using 1 μl of the positive samples and 5 μl of blanks/negatives for each pool (Alberdi et al., 2018).”
From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? (2019, background): “While mock communities are useful to identify errors and estimate error rates, the conclusions cannot easily be translated to realistic environments with rich and complex communities (Alberdi et al., 2018).”
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish (2020, background): “…existing technical issues, the choice of PCR primers for amplification of target sequences (i.e. barcodes) is possibly one of the most influential factors in determining the detection probability of specific species or taxonomic groups (i.e. community survey; Alberdi et al., 2018; Freeland, 2017).”
A practical guide to DNA metabarcoding for entomological ecologists (2020, background): “Using PCR replicates can reduce false-negative detections (Alberdi et al., 2018), and five to 10 replicates are particularly effective in recovering rare taxa from a given sample (Ficetola et al.”