Cited by 765Environmental DNA in Biodiversity StudiesInvertebrate Taxonomy and EcologyMicrobial Community Ecology and Physiology

The DOI matches its Crossref record; 59 of the 60 references it cites were found in a registry or an index; none of the 35 sources its claims cite is checked for support yet.

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

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Elbrecht, Vasco, Leese, Florian·2015·PLOS ONE

DOI 10.1371/journal.pone.0130324PMC PMC4496048

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Abstract

Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI) barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads). Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I). Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II). Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR-based metabarcoding assessments of biodiversity should rely on presence-absence metrics.

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TL;DR

This study developed and tested a replicated COI metabarcoding protocol for freshwater macroinvertebrates, using bulk DNA extraction and Illumina MiSeq sequencing. It found a strong biomass–read relationship within a single species, but strong species-specific primer bias across taxa, concluding that PCR-based metabarcoding cannot reliably quantify species abundance or biomass and should be used for presence–absence assessments.

Key findings

In experiment I, all 31 *Dinocras cephalotes* specimens were recovered across ten replicates, including the smallest specimen at 0.023% (0.145 mg) of total biomass; specimen biomass and sequence abundance showed a highly significant positive linear correlation in all ten replicates (p<0.001, R² = 0.65).
In experiment II, 83% (43/52) of taxa were reliably recovered; 34 taxa were recovered in all ten replicates. Recovery by group was Ephemeroptera 7/8 (88%), Plecoptera 4/4 (100%), Trichoptera 13/15 (86%), Diptera 7/8 (88%), and Others 12/17 (71%).
Despite similar biomass, sequence abundance varied by four orders of magnitude among taxa, and there was no correlation between taxon biomass and number of recovered sequences. Primer efficiency was highly species-specific, preventing straightforward abundance or biomass inference.
LCO and HCO sequencing direction had small effects on final sequence abundance (2.7% and 4.4% differences in experiments I and II), though LCO was 34% more frequent in experiment I (p = 0.006) and no primer bias was detected in experiment II (p = 0.41).

Methods

Two controlled experiments with ten replicates each were sequenced on two independent MiSeq runs using 300-bp paired-end reads; experiment I used 31 *D. cephalotes* stonefly specimens spanning three orders of magnitude in biomass, and experiment II used 52 freshwater invertebrate taxa with similar tissue biomass.
DNA was extracted in bulk, amplified in a single PCR step with tagged fusion primers based on standard COI LCO1490/HCO2198, purified, and directly sequenced; experiment I used 1.4% and 20% tissue aliquots, while experiment II pooled roughly equal tissue amounts per taxon.
Bioinformatic analysis used demultiplexing, cutadapt primer removal, read concatenation, blastn against reference haplotypes for experiment I, and UPARSE OTU clustering at 97% identity with BOLD identification for experiment II; sequence counts were normalised to total sequence abundance and tissue weight.

Limitations

The paper states that PCR-based metabarcoding cannot accurately estimate species biomass or even abundance in diverse environmental samples because primer efficiency is highly species-specific; it recommends presence–absence metrics and notes that PCR-free approaches are needed for biomass estimates.
The paper states that only 83% of taxa were recovered with one universal COI primer pair, that barcode reference databases remain incomplete, that DNA-based assessments cannot assign biological traits, and that PCR replication effects were not evaluated due to a small number of replicates.
Evident from the text: the experiments are limited to freshwater macroinvertebrates from western Germany and a specific MiSeq/COI Folmer protocol; some morphotaxa were identified only to family or order and contained multiple MOTUs, so species-level amplification behaviour may be more variable than the morphotaxon-level summaries suggest.

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Crossref · 10.1371/journal.pone.0130324

Cites

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Probably not a substantial claim. 23
It may state two separate claims as one. 23

In the paper
“Furthermore, we used a universal COI primer with a broad target range [41], and only 17% of taxa went undetected.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [41] O Folmer, 1994, DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Mol Marine Biol Biotechnol
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In the paper
“different species within a genus or subfamily can have different ecological preferences and stress tolerances and belong to different functional feeding groups [11,12] see [13] for review.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [11] Merritt RW, Berg MB, Cummins KW. An Introduction to the Aquatic Insects of North America. 2009.
- Not checked yetcites [12] SU Pauls, 2008, Grazers, shredders and filtering carnivores—The evolution of feeding ecology in Drusinae (Trichoptera: Limnephilidae): Insights from a molecular phylogeny, Mol Phylogenet Evol source
- Not checked yetcites [13] FC Jones, 2008, Taxonomic sufficiency: The influence of taxonomic resolution on freshwater bioassessments using benthic macroinvertebrates, Environ Rev source
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It may state two separate claims as one.
In the paper
“many benthic invertebrate larvae are difficult to identify at the species level, and thus the most practical taxonomic level for the identification of these organisms is often only the genus or family [10].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [10] P Haase, 2010, First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results, J North Am Benthol Soc source
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“DNA barcoding allows for standardized and accurate species identification [15–18].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [15] PDN Hebert, 2003, Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species, Proc R Soc Lond B Biol Sci source
- Not checked yetcites [16] X Zhou, 2009, Towards a comprehensive barcode library for arctic life—Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada, Front Zool source
- Not checked yetcites [17] X Zhou, 2010, Ephemeroptera, Plecoptera, and Trichoptera fauna of Churchill (Manitoba, Canada): insights into biodiversity patterns from DNA barcoding, J North Am Benthol Soc source
- Not checked yetcites [18] BW Sweeney, 2011, Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?, J North Am Benthol Soc source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“frequent identification errors occur and many specimens are not detected in samples [10]”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [10] P Haase, 2010, First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results, J North Am Benthol Soc source
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“All analyses were performed with ten replicates to improve statistical robustness.”
- Also stated in: § Abstract · plain
  “Each experiment was replicated ten times to maximise statistical power.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Stein and co-authors showed that ten of 16 assessment metrics had higher statistical power using DNA barcoding than morphological assessment [14].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [14] ED Stein, 2014, Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?, PLoS ONE source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“For animals, a 658-bp standardized fragment of the mitochondrial gene COI (cytochrome c oxidase subunit 1) is typically used [19].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [19] PDN Hebert, 2003, Biological identifications through DNA barcodes, Proc R Soc Lond B Biol Sci source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Several studies show that DNA-based assessments are superior to morphological assessments in freshwater ecosystems (e.g., [14,25,33])”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion
What the sources say
- Not checked yetcites [14] ED Stein, 2014, Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?, PLoS ONE source
- Not checked yetcites [25] JK Jackson, 2014, Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications, Freshw Sci source
- Not checked yetcites [33] Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B. Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Mol Ecol Resour. 2014; 1–17. <comment>doi: 10.1111/1755-0998.12336</comment> source
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The efforts of large national and international barcoding consortia (BOLD, iBOL, and GBOL) have contributed to a substantial increase in both the size and quality of reference databases [56]”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [56] P Taberlet, 2012, Towards next-generation biodiversity assessment using DNA metabarcoding, Mol Ecol source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“we are confident that metabarcoding will widely replace present biomonitoring methods over time because 1) it has a higher taxonomic resolution [14], 2) it is cost efficient and fast and, most importantly, 3) it reduces human bias enabling comparisons among studies [57].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [14] ED Stein, 2014, Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?, PLoS ONE source
- Not checked yetcites [57] Y Ji, 2013, Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding, Ecol Lett source
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Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“Piñol et al. [39] proposed a relationship between biomass and sequence reads, but did not systematically examine this hypothesis.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Experiment I: Relationship between specimen biomass and sequence abundance
What the sources say
- Not checked yetcites [39] Piñol J, Mir G, Gomez-Polo P, Agustí N. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol Ecol Resour. 2014; 1–12. <comment>doi: 10.1111/1755-0998.12355</comment> source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“However, while this approach could have comparable taxonomic resolution as the COI barcode, it is currently limited by the lack of reference databases [55].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [55] LJ Clarke, 2014, Environmental metabarcodes for insects: in silicoPCR reveals potential for taxonomic bias, Mol Ecol Resour source
Strength:hedged· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A combination of both data types, i.e., DNA species barcodes and ecological traits, will maximise the power of metabarcoding for the reliable assessment of ecosystem responses under stress and for biomonitoring.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim. It may be too vague to check against evidence.
- Rests on an assumption: DNA-based assessments cannot assign biological traits to species.

38 of 38

The paper relies on this without support.
Precise estimates of biomass with respect to specimen recovery and primer bias have not been performed.
“Precise estimates of biomass with respect to specimen recovery and primer bias have not been performed.”
The paper relies on this without support.
COI amplicons are typically similar in base composition.
“COI amplicons are typically similar in base composition; therefore, three strategies were used to increase sequence diversity.”
The paper relies on this without support.
Sanger sequencing requires that each specimen is processed individually in the laboratory, which is costly and extremely time-consuming for routine community assessments involving hundreds or thousands of specimens per sample.
“However, Sanger sequencing requires that each specimen is processed individually in the laboratory, which is costly and extremely time-consuming for routine community assessments involving hundreds or thousands of specimens per sample.”
The paper relies on this without support.
Benthic indicator organisms vary in biomass, and this variation depends on taxonomic group and life stage.
“Benthic indicator organisms vary in biomass, and this variation depends on taxonomic group and life stage.”
The paper relies on this without support.
Morphotaxa could often only be identified at family or order level, and several species per morphotaxon may occur in the sampled aquatic habitats even at the same habitat patch.
“This was expected, as morphotaxa could often only be identified at family or order level, and several species per morphotaxon may occur in the sampled aquatic habitats even at the same habitat patch.”
The paper relies on this without support.
Stochastic effects increase with reduced specimen biomass.
“This result is expected because stochastic effects increase with reduced specimen biomass.”
The paper relies on this without support.
Currently, the monitoring of freshwater ecosystems is based on abundance metrics, which cannot be generated using the metabarcoding solutions currently available.
“Currently, the monitoring of freshwater ecosystems is based on abundance metrics, which cannot be generated using the metabarcoding solutions currently available.”
The paper relies on this without support.
All assessment protocols rely on reference catalogues against which inventory data of a species from an ecosystem are compared.
“All assessment protocols rely on reference catalogues against which inventory data of a species from an ecosystem are compared.”
The paper relies on this without support.
Changes in species traits in a community (e.g. functional feeding groups, tolerance against pollution) are used as indicator values to evaluate the biological significance of inferred community changes.
“In particular, changes in species traits in a community (e.g. functional feeding groups, tolerance against pollution) are used as indicator values to evaluate the biological significance of inferred community changes.”
The paper relies on this without support.
DNA-based assessments cannot assign biological traits to species.
“However, DNA-based assessments cannot assign biological traits to species.”

10 of 10

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All 52 taxa assigned OTUs despite taxa going undetected
Minor
The paper says OTUs were reliably assigned to all 52 taxa, but later says 17% of the taxa went undetected. Undetected taxa cannot also have been assigned OTUs.

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Keskin, E., Ünal, E. M., & Atar, H. H. (2016) · Biochemical Systematics and Ecology · doi:10.1016/j.bse.2016.05.020 · Cited by 39
Estimating belowground plant abundance with DNA metabarcoding
Matesanz, S., Pescador, D. S., Pías, B., Sánchez, A. M., Chacón‐Labella, J., Illuminati, Á., de la Cruz, M., López‐Angulo, J., Marí‐Mena, N., Vizcaíno, A., et al. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13049 · Cited by 38
“…use the observed percentage of DNA sequences to estimate species’ abundances in communities of microbes (Amend, Seifert, & Bruns, 2010), stoneflies (Elbrecht & Leese, 2015), fish and amphibians (Evans et al., 2016; Pont et al., 2018), zooplankton (Harvey, Johnson, Fisher, Peterson, & Vrijenhoek,…”
BackgroundInfluential
Gaining ecological insight on dietary allocation among horseshoe bats through molecular primer combination
Aldasoro, M., Garin, I., Vallejo, N., Baroja, U., Arrizabalaga‐Escudero, A., Goiti, U., & Aihartza, J. (2019) · PLoS ONE · doi:10.1371/journal.pone.0220081 · Cited by 39
Macroinvertebrate community diversity and habitat quality relationships along a large river from targeted eDNA metabarcode assays
Marshall, N. T., & Stepien, C. A. (2020) · Environmental DNA · doi:10.1002/edn3.90 · Cited by 40
eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters
García‐Vázquez, E., Georges, O., Fernández, S., & Ardura, A. (2021) · Scientific Reports · doi:10.1038/s41598-021-86731-z · Cited by 43
Bats actively track and prey on grape pest populations
Baroja, U., Garin, I., Vallejo, N., Aihartza, J., Rebelo, H., & Goiti, U. (2021) · Ecological Indicators · doi:10.1016/j.ecolind.2021.107718 · Cited by 39
Metabarcoding on planktonic larval stages: an efficient approach for detecting and investigating life cycle dynamics of benthic aliens
Couton, M., Comtet, T., Cam, S. L., Corre, E., & Viard, F. (2019) · Management of Biological Invasions · doi:10.3391/mbi.2019.10.4.06 · Cited by 41
Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife
Klymus, K. E., Richter, C. A., Thompson, N. L., & Hinck, J. E. (2017) · Diversity · doi:10.3390/d9040054 · Cited by 39
“It has been argued that primer and other processing biases will prevent the ability to infer estimates of abundance or relative biomass from metabarcoding eDNA samples [41].”
Background
Evaluating next‐generation sequencing (NGS) methods for routine monitoring of wild bees: Metabarcoding, mitogenomics or NGS barcoding
Gueuning, M., Ganser, D., Blaser, S., Albrecht, M., Knop, E., Praz, C. J., & Frey, J. E. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13013 · Cited by 39
“…very nature of the amplification steps involved in MB, this method can be subject to heavy bias, making quantifications doubtable (Dowle, Pochon, Banks, Shearer, & Wood, 2016; Elbrecht & Leese, 2015; Elbrecht et al., 2016; Piñol, Mir, Gomez-Polo, & Agustí, 2015; Tang et al., 2015; Yu et al., 2012).”
Method
Multi-marker DNA metabarcoding reflects tardigrade diversity in different habitats
Topstad, L., Guidetti, R., Majaneva, M., & Ekrem, T. (2020) · Genome · doi:10.1139/gen-2019-0218 · Cited by 43
Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis
Arribas, P., Andújar, C., Bidartondo, M. I., Bohmann, K., Coissac, É., Creer, S., deWaard, J. R., Elbrecht, V., Ficetola, G. F., Goberna, M., et al. (2021) · Molecular Ecology · doi:10.1111/mec.15797 · Cited by 41
“…speaking, it has been suggested that the most conservative approach is to treat DNA metabarcoding data as presence– absence data after applying a high filtering threshold based on read relative abundance to mitigate the impact of the false positives (Elbrecht et al., 2015; Taberlet et al., 2012).”
MethodSelf-citation
Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)
Λεοντίδου, Κ., Vokou, D., Sandionigi, A., Bruno, A., Lazarina, M., Groeve, J. D., Li, M., Varotto, C., Girardi, M., Casiraghi, M., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-97619-3 · Cited by 38
Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal
Stapleton, T. E., Weinstein, S. B., Greenhalgh, R., & Dearing, M. D. (2022) · Molecular Ecology Resources · doi:10.1111/1755-0998.13643 · Cited by 38
Diatom eDNA metabarcoding and morphological methods for bioassessment of karstic river
Kulaš, A., Udovič, M. G., Tapolczai, K., Žutinić, P., Orlić, S., & Levkov, Z. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2022.154536 · Cited by 38
The use of environmental DNA to monitor impacted coastal estuaries
DiBattista, J. D., Fowler, A. M., Riley, I. J., Reader, S. E., Hay, A. C., Parkinson, K., & Hobbs, J. (2022) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2022.113860 · Cited by 37
A DNA barcode database of Australia’s freshwater macroinvertebrate fauna
Carew, M. E., Nichols, S. J., Batovska, J., Clair, R. S., Murphy, N. P., Blacket, M. J., & Shackleton, M. E. (2017) · Marine and Freshwater Research · doi:10.1071/mf16304 · Cited by 41
Slippage of degenerate primers can cause variation in amplicon length
Elbrecht, V., Hebert, P. D. N., & Steinke, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-29364-z · Cited by 39
“Only sequences of the randomly selected mock community “B” were analyzed from Elbrecht & Leese 2015.”
MethodSelf-citation
Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data
Buchner, D., Beermann, A. J., Laini, A., Rolauffs, P., Vitecek, S., Hering, D., & Leese, F. (2019) · PLoS ONE · doi:10.1371/journal.pone.0226547 · Cited by 36
Self-citation
Tracking seasonal changes in diversity of pollen allergen exposure: Targeted metabarcoding of a subtropical aerobiome
Campbell, B. C., Kouba, J. A., Timbrell, V. L., Noor, M. J., Massel, K., Gilding, E. K., Angel, N. Z., Kemish, B., Hugenholtz, P., Godwin, I. D., et al. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.141189 · Cited by 37
Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics
Buchner, D., Haase, P., & Leese, F. (2021) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.5.67533 · Cited by 39
Self-citation
Disentangling bias for non-destructive insect metabarcoding
Martoni, F., Piper, A. M., Rodoni, B. C., & Blacket, M. J. (2022) · PeerJ · doi:10.7717/peerj.12981 · Cited by 36
Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa
Yang, J., Zhang, L., Mu, Y., Wang, J., Yu, H., & Zhang, X. (2023) · Environment International · doi:10.1016/j.envint.2023.107950 · Cited by 36
18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability
Waraniak, J. M., Marsh, T. L., & Scribner, K. T. (2019) · Ecology and Evolution · doi:10.1002/ece3.4857 · Cited by 35
“However, the relationship between biomass and number of sequence reads can be highly variable among taxa due to amplification bias of the primers (Albaina et al., 2016; Elbrecht & Leese, 2015).”
BackgroundMethodInfluential
Pooling size sorted Malaise trap fractions to maximize taxon recovery with metabarcoding
Elbrecht, V., Bourlat, S. J., Hörren, T., Lindner, A., Mordente, A., Noll, N. W., Schäffler, L., Sorg, M., & Zizka, V. M. A. (2021) · PeerJ · doi:10.7717/peerj.12177 · Cited by 45
“While there is a loose correlation between biomass and read abundance ( Lamb et al., 2019 ), metabarcoding results are often skewed by primer bias ( Elbrecht & Leese, 2015 ; Piñol et al., 2015 ; Krehenwinkel et al., 2017 ), mitochondrial copy number variation ( Braukmann et al., 2019 ; Deagle et…”
Self-citation
Metabarcoding Techniques for Assessing Biodiversity of Marine Animal Forests
Wangensteen, O. S., & Turón, X. (2017) · Springer eBooks · doi:10.1007/978-3-319-21012-4_53 · Cited by 35
DNA-Based Herbal Teas’ Authentication: An ITS2 and psbA-trnH Multi-Marker DNA Metabarcoding Approach
Frigerio, J., Agostinetto, G., Mezzasalma, V., Mattia, F. D., Labra, M., & Bruno, A. (2021) · Plants · doi:10.3390/plants10102120 · Cited by 35
“For example, it has already been reported in the literature that primers have a differential affinity for some species, leading to preferential amplification of some taxa, and substantial differences in selectivity among different primers [22,33,34].”
Background
Insights into the diet and trophic ecology of white sharks (Carcharodon carcharias) gained through DNA metabarcoding analyses of cloacal swabs
Clark, Z. S. R., Fish, J. J., Butcher, P. A., Holland, O. J., Sherman, C. D. H., Rizzari, J. R., Weeks, A. R., & Miller, A. D. (2023) · Environmental DNA · doi:10.1002/edn3.454 · Cited by 34
Phytoplankton community composition in relation to environmental variability in the Urdaibai estuary (SE Bay of Biscay): Microscopy and eDNA metabarcoding
Bilbao, J., Pavloudi, C., Blanco-Rayón, E., Franco, J., Madariaga, I., & Seoane, S. (2023) · Marine Environmental Research · doi:10.1016/j.marenvres.2023.106175 · Cited by 35
DNA metabarcoding and morphological identification reveal similar richness, taxonomic composition and body size patterns among flying insect communities
Remmel, N., Buchner, D., Enß, J., Hartung, V., Leese, F., Welti, E. A. R., Sinclair, J. S., & Haase, P. (2024) · Insect Conservation and Diversity · doi:10.1111/icad.12710 · Cited by 33
“…limited to presence – absence data as it generally cannot provide accurate information about taxon absolute abundances, although efforts to rectify this issue are ongoing (e. g., Elbrecht & Leese, 2015; Elbrecht, Vamos, et al., 2017; Nichols et al., 2018; Shelton et al., 2023; Sickel et al., 2023).”
BackgroundMethodSelf-citation
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity
Salis, R. K., Sunde, J., Gubonin, N., Franzén, M., & Forsman, A. (2024) · Molecular Ecology Resources · doi:10.1111/1755-0998.14018 · Cited by 38
“Therefore, metabarcoding has often been shown to only provide presence–absence data rather than reliable information on relative abundance (Creedy et al., 2019; Elbrecht & Leese, 2015; Piñol et al., 2015 ).”
Diet and trophic interactions of a circumglobally significant gelatinous marine zooplankter,Dolioletta gegenbauri(Uljanin, 1884)
Walters, T. L., Lamboley, L. M., López‐Figueroa, N. B., Rodríguez‐Santiago, Á. E., Gibson, D. M., & Frischer, M. E. (2018) · Molecular Ecology · doi:10.1111/mec.14926 · Cited by 34
“…bias is well known to occur, especially when general “universal” primers are utilized due to differences in primer targeting specificity, efficiency and amplification interference by complex amplification substrates (Brooks, Edwards, & Harwich, 2015; Elbrecht & Leese, 2015; Polz & Cavanaugh, 1998).”
Background
MAUI‐seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction
Fields, B., Moeskjær, S., Friman, V., Andersen, S. U., & Young, J. P. W. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13294 · Cited by 34
“3 Many studies have evaluated the extent of PCR-based amplification errors and bias for HTAS diversity studies [4, 6, 7, 11].”
Background
Mock samples resolve biases in diversity estimates and quantitative interpretation of zooplankton metabarcoding data
Ershova, E. A., Wangensteen, O. S., & Falkenhaug, T. (2023) · Marine Biodiversity · doi:10.1007/s12526-023-01372-x · Cited by 33
“Several previous studies have reported moderate to good correlations of relative read numbers to relative biomass in zooplankton for several genetic markers, including COI (Elbrecht and Leese 2015; Ershova et al. 2021; Matthews et al. 2021; Yang et al. 2017).”
BackgroundInfluential
Abundance estimation with DNA metabarcoding – recent advancements for terrestrial arthropods
Sickel, W., Zizka, V. M. A., Scherges, A. M., Bourlat, S. J., & Dieker, P. (2023) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.7.112290 · Cited by 34
The challenges and promises of genetic approaches for ballast water management
Rey, A., Basurko, O. C., & Rodríguez‐Ezpeleta, N. (2017) · Journal of Sea Research · doi:10.1016/j.seares.2017.06.001 · Cited by 33
When to use next generation sequencing or diagnostic PCR in diet analyses
Rubbmark, O. R., Sint, D., Cupic, S., & Traugott, M. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12974 · Cited by 35
“…NGS metabarcoding data sequence numbers can be misleading (Yu et al., 2012; Deagle, Thomas, Shaffer, Trites, & Jarman, 2013, Elbrecht & Leese, 2015; Ficetola et al., 2015), and because of this, even though NGS metabarcoding data may have quantitative aspects, it is usually treated as…”
Background
The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada
Edge, T. A., Baird, D. J., Bilodeau, G. J., Gagné, N., Greer, C. W., Konkin, D. J. F., Newton, G., Séguin, A., Beaudette, L. A., Bilkhu, S., et al. (2019) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2019.135906 · Cited by 36
“For example, metagenomics techniques are still unable to provide complete characterization of all microbial and invertebrate biodiversity in soil and water samples (Elbrecht and Leese, 2015; Nesme et al., 2016; Rodriguez et al., 2018; Oliverio et al., 2018; Pawlowski et al., 2018).”
Background
Targeted non-invasive bioindicator species detection in eDNA water samples to assess and monitor the integrity of vulnerable alpine freshwater environments
Blattner, L. A., Ebner, J. N., Zopfi, J., & von Fumetti, S. (2021) · Ecological Indicators · doi:10.1016/j.ecolind.2021.107916 · Cited by 31
“…sequence databases (Elbrecht et al., 2017; Weigand et al., 2019), difficulties to reliably quantify species abundances (Beng and Corlett, 2020; Elbrecht and Leese, 2015), and the need of demanding expert knowledge can diminish the feasibility and implementation in applied environmental…”
Background
Predator-prey interactions of terrestrial invertebrates are determined by predator body size and species identity.
Kuile, A. T., Apigo, A., An, B., DiFiore, B. P., Forbes, E. S., Lee, M. J., Orr, D., Preston, D. L., Behm, R., Bogar, T. A., et al. (2022) · Ecology · doi:10.1002/ecy.3634 · Cited by 26
“…body size data had high resolution for the predators included in this study, we are still limited in knowing the abundance or realized size of prey items consumed by these predators because read abundance may not accurately correspond to prey biomass (Elbrecht et al., 2017; Elbrecht & Leese, 2015).”
Background
Evaluation of DNA metabarcoding using Oxford Nanopore sequencing for authentication of mixed seafood products
Toxqui-Rodríguez, S., Vanhollebeke, J., & Derycke, S. (2022) · Food Control · doi:10.1016/j.foodcont.2022.109388 · Cited by 33
Validation of Environmental DNA for Estimating Proportional and Absolute Biomass
Ledger, K. J., Hicks, M. B. R., Hurst, T. P., Larson, W. A., & Baetscher, D. S. (2024) · Environmental DNA · doi:10.1002/edn3.70030 · Cited by 32
Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding
Wangensteen, O. S., Cebrián, E., Palacín, C., & Turón, X. (2017) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2017.11.033 · Cited by 32
“Besides marker choice and processing protocols, one of the most contentious issues in eukaryote metabarcoding is the quantitative value of the data (Elbrecht and Leese, 2015; Wares and Pappalardo, 2016; Creer et al., 2016).”
Background
Numerical methods for sedimentary‐ancient‐DNA‐based study on past biodiversity and ecosystem functioning
Chen, W., & Ficetola, G. F. (2020) · Environmental DNA · doi:10.1002/edn3.79 · Cited by 32
“…different match with primers among species, differences in eDNA shedding, and multiple technical parameters (e.g., GC content, polymerase mixes, and number of PCR cycles); therefore, all the results must be interpreted with caution (Elbrecht & Leese, 2015; Fonseca, 2018; Nichols et al., 2018).”
Result
Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages
Sigsgaard, E. E., Olsen, K., Hansen, M. D. D., Hansen, O. L. P., Høye, T. T., Svenning, J., & Thomsen, P. F. (2020) · Molecular Ecology · doi:10.1111/mec.15734 · Cited by 32
“The initial heat deactivation, denaturation and extension steps were chosen based on the guidelines for the HotStarTaq Master Mix, while the annealing temperature followed Elbrecht and Leese (2015).”
Method
Meiofauna as a valuable bioindicator of climate change in the polar regions
Leasi, F., Sevigny, J. L., & Hassett, B. T. (2020) · Ecological Indicators · doi:10.1016/j.ecolind.2020.107133 · Cited by 32
Single-cell metabarcoding reveals biotic interactions of the Arctic calcifier Neogloboquadrina pachyderma with the eukaryotic pelagic community
Greco, M., Morard, R., & Kučera, M. (2021) · Journal of Plankton Research · doi:10.1093/plankt/fbab015 · Cited by 32
Environmental DNA of preservative ethanol performed better than water samples in detecting macroinvertebrate diversity using metabarcoding
Wang, Y., Chen, K., Gao, J., Wang, M., Dong, J., Xie, Y., Giesy, J. P., Jin, X., & Wang, B. (2021) · Diversity and Distributions · doi:10.1111/ddi.13284 · Cited by 30
“ESVs with sequence abundances greater than 0.005% in each sample (Elbrecht & Leese, 2015; Macher et al., 2018) were retained.”
Influential
Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding
Hestetun, J. T., Lanzén, A., & Dahlgren, T. G. (2021) · PeerJ · doi:10.7717/peerj.11619 · Cited by 32
Molecular gut content analysis indicates the inter‐ and intra‐guild predation patterns of spiders in conventionally managed vegetable fields
Saqib, H. S. A., Liang, P., You, M., & Gurr, G. M. (2021) · Ecology and Evolution · doi:10.1002/ece3.7772 · Cited by 32
“…whole prey DNA fragments in the gut of predators, for example, the sequencing of prey species using a DNA barcode or a fragment of mitochondrial cytochrome c oxidase subunit I (COI) gene (Brandon- Mong et al., 2015; Elbrecht & Leese, 2015; Hamad et al., 2014; Hebert et al., 2003; Mitchell, 2008).”
Method
Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem
Huang, J., Miao, X., Wang, Q., Menzel, F., Tang, P., Yang, D., Wu, H. Y., & Vogler, A. P. (2022) · Ecology and Evolution · doi:10.1002/ece3.8535 · Cited by 31
“…animal guts, macrozoobenthos in marine and fresh water, and invertebrates from soil and Malaise traps, emerging as a promising way of advancing biodiversity research (Arribas et al., 2016; Elbrecht & Leese, 2015; Ji et al., 2013; Morinière et al., 2019; Orgiazzi et al., 2015; Zhang et al., 2016).”
Background
Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera)
Basset, Y., Hajibabaei, M., Wright, M., Castillo, A. M., Donoso, D. A., Segar, S. T., Souto‐Vilarós, D., Soliman, D., Roslin, T. V., Smith, M. A., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-14915-2 · Cited by 39
Environmental DNA metabarcoding of rivers: Not all eDNA is everywhere, and not all the timePreprint
Macher, J.-N., & Leese, F. (2017) · bioRxiv · doi:10.1101/164046 · Cited by 30
Self-citation
Detection of critically endangered marine species with dwindling populations in the wild using eDNA gives hope for sawfishes
Bonfil, R., Barreto, P. P., Vargas, O. U. M., Ricaño-Soriano, M., & Díaz‐Jáimes, P. (2021) · Marine Biology · doi:10.1007/s00227-021-03862-7 · Cited by 31
Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples
Ferreira, A. O., Azevedo, O. M., Barroso, C., Duarte, S., Egas, C., Fontes, J. T., Ré, P., Santos, A. M. P., & Costa, F. O. (2024) · Scientific Reports · doi:10.1038/s41598-024-69963-7 · Cited by 37
“However, the use of COI primers of a broad taxonomic spectrum may favour non-specific amplification and primer bias 21,65 .”
Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers
Rivera, S. F., Vasselon, V., Mary, N., Monnier, O., Rimet, F., & Bouchez, A. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.144208 · Cited by 35
DNA metabarcoding-based diet survey for the Eurasian otter (Lutra lutra): Development of a Eurasian otter-specific blocking oligonucleotide for 12S rRNA gene sequencing for vertebrates
Kumari, P., Dong, K., Eo, K.-Y., Lee, W.-S., Kimura, J., & Yamamoto, N. (2019) · PLoS ONE · doi:10.1371/journal.pone.0226253 · Cited by 30
eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
Schwentner, M., Zahiri, R., Yamamoto, S., Husemann, M., Kullmann, B., & Thiel, R. (2021) · PLoS ONE · doi:10.1371/journal.pone.0250452 · Cited by 32
“To assemble OTUs for the BLAST approach, we followed in parts the methodology laid out in [33] (see S1 File for a detailed list of all employed steps and commands).”
Method
Recommendations for interpreting zooplankton metabarcoding and integrating molecular methods with morphological analyses
Matthews, S. A., Goetze, E., & Ohman, M. D. (2021) · ICES Journal of Marine Science · doi:10.1093/icesjms/fsab107 · Cited by 30
“While species richness is an important aspect of diversity, abundance and demographic structure are also important for understanding ecosystem dynamics (Elbrecht and Leese, 2015).”
Background
Sponging up diversity: Evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community
Timmers, M. A. V., Vicente, J., Webb, M. K., Jury, C. P., & Toonen, R. J. (2020) · Environmental DNA · doi:10.1002/edn3.163 · Cited by 35
Experimental validation of taxon‐specific mini‐barcode primers for metabarcoding of zooplankton
Govender, A., Singh, S. P., Groeneveld, J. C., Pillay, S., & Willows‐Munro, S. (2021) · Ecological Applications · doi:10.1002/eap.2469 · Cited by 29
A glance into the black box: Novel species-specific quantitative real-time PCR assays to disentangle aquatic hyphomycete community composition
Baudy, P., Zubrod, J. P., Röder, N., Baschien, C., Feckler, A., Schulz, R., & Bundschuh, M. (2019) · Fungal ecology · doi:10.1016/j.funeco.2019.08.002 · Cited by 29
Effective detection of environmental DNA from the invasive American bullfrog
Lin, M., Zhang, S., & Yao, M. (2019) · Biological Invasions · doi:10.1007/s10530-019-01974-2 · Cited by 30
DNA metabarcoding improves the detection of multiple stressor responses of stream invertebrates to increased salinity, fine sediment deposition and reduced flow velocity
Beermann, A. J., Werner, M., Elbrecht, V., Zizka, V. M. A., & Leese, F. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.141969 · Cited by 27
Self-citation
Sucked in by eDNA – a promising tool for complementing riverine assessment of freshwater fish communities in Aotearoa New Zealand
David, B. O., Fake, D. R., Hicks, A. S., Wilkinson, S., Bunce, M., Smith, J., West, D. W., Collins, K., & Gleeson, D. M. (2021) · New Zealand Journal of Zoology · doi:10.1080/03014223.2021.1905672 · Cited by 28
“However, the semi-quantitative signal evident in eDNAmonitoring data may have utility for estimating biomass in a temporally and/or spatially relative context when sufficient replication and sample quality control is employed (Elbrecht and Leese 2015).”
BackgroundMethodInfluential
Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity
Bulman, S. R., McDougal, R. L., Hill, K., & Lear, G. (2018) · Australasian Plant Pathology · doi:10.1007/s13313-018-0579-3 · Cited by 28
DNA metabarcoding of mock communities highlights potential biases when assessing Neotropical fish diversity
Hilário, H. O., Mendes, I. S., Sales, N. G., & Carvalho, D. C. (2023) · Environmental DNA · doi:10.1002/edn3.456 · Cited by 27
Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands
Theißinger, K., Kästel, A., Elbrecht, V., Makkonen, J., Michiels, S., Schmidt, S. I., Allgeier, S., Leese, F., & Brühl, C. A. (2018) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.2.21060 · Cited by 29
“To enhance data reliability, sequences matched to the respective OTU had to occur in both replicates and exceed the 0.003% threshold sequence abundance to being considered in downstream analysis (Elbrecht and Leese 2015).”
InfluentialSelf-citation
How Does eDNA Compare to Traditional Trapping? Detecting Mosquito Communities in South-African Freshwater Ponds
Krol, L., van der Hoorn, B., Gorsich, E. E., Trimbos, K. B., van Bodegom, P. M., & Schrama, M. J. J. (2019) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00260 · Cited by 28
Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol
Gauthier, M., Konecny‐Dupré, L., Nguyen, A., Elbrecht, V., Datry, T., Douady, C. J., & Tristan, L. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13088 · Cited by 34
“The 52 taxa mock communities were designed by Elbrecht and Leese (2015).”
BackgroundMethodInfluentialSelf-citation
Environmental DNA simultaneously informs hydrological and biodiversity characterization of an Alpine catchment
Mächler, E., Salyani, A., Walser, J., Larsen, A., Schaefli, B., Altermatt, F., & Ceperley, N. (2021) · Hydrology and earth system sciences · doi:10.5194/hess-25-735-2021 · Cited by 27
Finding the perfect pairs: A matchmaking of plant markers and primers for multi‐marker eDNA metabarcoding
Prieto, A. E., Hardion, L., Debortoli, N., & Beisel, J. (2024) · Molecular Ecology Resources · doi:10.1111/1755-0998.13937 · Cited by 28
Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species
Scott, R., Zhan, A., Brown, E. A., Chain, F. J. J., Cristescu, M. E., Gras, R., & MacIsaac, H. J. (2018) · Evolutionary Applications · doi:10.1111/eva.12604 · Cited by 26
“Previous studies covering different taxa, amplified fragments and applications have utilized sequence processing strategies that included more stringent Q filtering, typically between 20 and 30 (Bista et al., 2017; Elbrecht & Leese, 2015; Hänfling et al., 2016).”
Method
Molecular diet analysis reveals predator–prey community dynamics and environmental factors affecting predation of larval lake sturgeon Acipenser fulvescens in a natural system
Waraniak, J. M., Baker, E. A., & Scribner, K. T. (2018) · Journal of Fish Biology · doi:10.1111/jfb.13726 · Cited by 26
DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds
Sun, Z., Majaneva, M., Sokolova, E., Rauch, S., Meland, S., & Ekrem, T. (2019) · Ecology and Evolution · doi:10.1002/ece3.5503 · Cited by 25
“A major challenge in (PCR‐based) metabarcoding is that it does not provide quantitative abundance data, especially in the case of di‐ verse community samples (Elbrecht & Leese, 2015).”
Background
A fecal sequel: Testing the limits of a genetic assay for bat species identification
Walker, F. M., Tobin, A., Simmons, N. B., Sobek, C. J., Sanchez, D. E., Chambers, C. L., & Fofanov, V. Y. (2019) · PLoS ONE · doi:10.1371/journal.pone.0224969 · Cited by 26
“Primer bias is expected when a single primer set is used across a taxonomic group, and can result in a large variance in read numbers [45].”
Background
DNA metabarcoding of zooplankton communities: species diversity and seasonal variation revealed by 18S rRNA and COI
Zhao, L., Zhang, X., Xu, M., Mao, Y., & Huang, Y. (2021) · PeerJ · doi:10.7717/peerj.11057 · Cited by 28
Disentangling higher trophic level interactions in the cabbage aphid food web using high-throughput DNA sequencing
Lefort, M.-C., Wratten, S. D., Cusumano, A., Varennes, Y., & Boyer, S. (2017) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.1.13709 · Cited by 25
“The detection of aphid DNA may have also been affected by primer bias (Piñol et al. 2014, Elbrecht and Leese 2015) potentially leading to preferential amplification of DNA from Figure 4.”
Background
A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms
Hernández‐Agreda, A., Leggat, W. P., & Ainsworth, T. D. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02146 · Cited by 26
“In generating a microbiome dataset, sample homogenization is an essential process within the DNA extraction (Elbrecht and Leese, 2015; Lear et al., 2018).”
Background
Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding
Rossel, S., Khodami, S., & Arbizu, P. M. (2019) · Frontiers in Marine Science · doi:10.3389/fmars.2019.00659 · Cited by 26
“Although there seems to be agreement that metabarcoding cannot estimate the absolute abundance of species in the samples (Elbrecht and Leese, 2015), our results show that the log(x+ 1) transformation is accurate in estimating at least the relative abundance of the species within samples.”
Result
A Molecular Approach to Explore the Background Benthic Fauna Around a Hydrothermal Vent and Their Larvae: Implications for Future Mining of Deep-Sea SMS Deposits
Klunder, L., de Stigter, H., Lavaleye, M., van Bleijswijk, J. D. L., van der Veer, H. W., Reichart, G., & Duineveld, G. (2020) · Frontiers in Marine Science · doi:10.3389/fmars.2020.00134 · Cited by 25
“The use of amplicon data for abundancy measurements has been disputed (Porazinska et al., 2010; Elbrecht and Leese, 2015; Barnes and Turner, 2016; Pawlowski et al., 2018).”
Background
Efficient assessment of nocturnal flying insect communities by combining automatic light traps and DNA metabarcoding
Mata, V. A., Ferreira, S., Campos, R. M., da Silva, L. P., Veríssimo, J., Corley, M. F. V., & Beja, P. R. (2020) · Environmental DNA · doi:10.1002/edn3.125 · Cited by 24
Development of a Specific Mini-Barcode From Plastome and its Application for Qualitative and Quantitative Identification of Processed Herbal Products Using DNA Metabarcoding Technique: A Case Study on Senna
Yu, X., Tan, W. C. C., Gao, H., Miao, L., & Tian, X. (2020) · Frontiers in Pharmacology · doi:10.3389/fphar.2020.585687 · Cited by 24
All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences
Jurburg, S. D., Keil, P., Singh, B. K., & Chase, J. M. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13401 · Cited by 28
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods
Arribas, P., Andújar, C., Bohmann, K., deWaard, J. R., Economo, E. P., Elbrecht, V., Geisen, S., Goberna, M., Krehenwinkel, H., Novotný, V., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac065 · Cited by 25
Self-citation

Authors: Elbrecht, V., & Leese, F.
Affiliations: Ruhr University Bochum (DE)
Corresponding author: Leese, Florian
ORCID: Elbrecht, Vasco
Leese, Florian
Venue: PLOS ONE
Publisher: Public Library of Science (PLoS)
Published: 2015-07-08
Volume: 10
Issue: 7
Pages: e0130324
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0130324
PMC: PMC4496048
OpenAlex: W1551951435
Semantic Scholar: 5b5925709b20821df1f956c4c737e5fadb1e8b43
Cited by: 765
References: 60
Citations by year: 2026: 75 · 2025: 73 · 2024: 49 · 2023: 69 · 2022: 71 · 2021: 91 · 2020: 75 · 2019: 73 · 2018: 108 · 2017: 51 · 2016: 26 · 2015: 3
FWCI: 56.82
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: PLoS ONE (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Topics: Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Invertebrate Taxonomy and Ecology
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: DNA metabarcoding, primer bias, species abundance estimation, COI barcoding, freshwater macroinvertebrates, Plecoptera, MiSeq sequencing, biodiversity assessment
MeSH terms: Animals, Electron Transport Complex IV, Diptera, DNA, Fresh Water, Haplotypes, Species Specificity, Reproducibility of Results, Polymerase Chain Reaction, Ecosystem, DNA Primers, Biomass, Biodiversity, DNA Barcoding, Taxonomic, High-Throughput Nucleotide Sequencing, Odonata

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Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

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