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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Cites

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Claims the paper makes

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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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None of the sources cited for this claim have been checked yet.
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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Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
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
“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
Strength:boosted· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✗ Checkable: fails✗ Load-bearing: fails✓ Based: passes
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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Malpartida, A., Piggott, M. P., Banks, S. C., Harford, A. J., Montgomery, K., van der Heyde, M., Nevill, P., & Andersen, A. N. (2026) · Environmental DNA · doi:10.1002/edn3.70245
Potential Impacts of Low Flows on Fish Foodscapes and Production in a Braided River
Stoffels, R. J., White, R. S. A., Török, G. T., Measures, R. J., Hogsden, K. L., Rose, A. F., Lambert, P. W., Bilewitch, J., Graham, S. E., Smith, L. M., et al. (2026) · River Research and Applications · doi:10.1002/rra.70137
Complementarity of ancient DNA and microfossil records in a marine sedimentary archive from the Arctic
Zimmermann, H., Limoges, A., Jackson, R., Lorenzen, E. D., & Ribeiro, S. (2026) · Marine Micropaleontology · doi:10.1016/j.marmicro.2026.102575
Structure et fonctionnement des colonies de Grand rhinolophe en Poitou-Charentes
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The detection of butterflies with DNA metabarcoding in Malaise trap bulk samples
Hoffmann, L., Buchner, D., Uhler, J., Haase, P., Müller, J., & Stoll, S. (2026) · Journal of Insect Conservation · doi:10.1007/s10841-026-00764-1
Dynamique des métacommunautés dans les têtes de bassin versant fragmentées : une perspective moléculaire
Gauthier, M. (2020) · theses.fr (ABES) · doi:10.70675/1aecfc48zabb1z4d30za665z5c7e02e5ae99
Biodiversity of the marine ecosystem and carbon flux around Kerguelen (Southern Ocean) : role of small phytoplankton at the single cell level
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High-throughput sequencing techniques for the detection and survey of marine non-indigenous species : a valuable addition to traditional methods ?
Couton, M. (2020) · theses.fr (ABES) · doi:10.70675/b1779c0czd493z4d41z807az5e71e566ac07
Metabarcoding in the abyss : uncovering deep-sea biodiversity through environmental DNA
Brandt, M. I. (2020) · doi:10.70675/0d2d4921z2c39z4b84zb3a5za8f479f89d14
Exploring temporal patterns of marine plankton communities in the Western English Channel through the analyses of morphological and metabarcoding time-series
Caracciolo, M. (2021) · theses.fr (ABES) · doi:10.70675/8723eba5z6f92z4a72z84dez1f21bbd2a07d
Side by side in space and time: Comparing standardized lake sampling methods and eDNA metabarcoding for assessing fish biodiversityPreprint
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L’ADN environnemental pour décrire les patrons de diversité des poissons à large échelle et informer la conservation
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Premières étapes dans l'interaction hôte-pathogène : rôle de l'immunité locale et innée
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Evaluate and quantify the effect of the management supported by the hunters' federations to the sedentary game fauna of lowlands and more widely on common and exceptional biodiversity in the French Mediterranean area
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Sánchez‐López, J. V., Pérez-Matus, A., Saenz‐Agudelo, P., Fernández, M., Wieters, E. A., Navarrete, S., Landaeta, M. F., Vargas, F., Ramirez, P., Cariman, P., et al. (2026) · Environmental DNA · doi:10.1002/edn3.70290
Assessing the temporal dynamics of airborne insect communities through DNA metabarcoding of aerial trap catches
Kim, M., Lee, W., Lee, H., Park, S., Kang, Y., Kim, J., Lee, J. Y., Oh, J., & Myeong, N. R. (2026) · Scientific Reports · doi:10.1038/s41598-026-51572-1
Bulk, water, and sediment eDNA metabarcoding reveal metric-driven differences in WFD macrozoobenthos ecological status classification in Slovakia
Šamulková, M., Beracko, P., Macko, P., Tuhrinová, K., Čiamporová‐Zaťovičová, Z., & ČIAMPOR, F. J. (2026) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.10.185694
Fine‐Scale Ecological Biomonitoring in a Large, Complex Agriculturally Impacted Watershed via eDNA Metabarcoding
Silva, B. S. M. L., Riley, A. C., Craiovan, E., Wright, M., Watson, K., Lapen, D. R., & Hajibabaei, M. (2026) · Molecular Ecology · doi:10.1111/mec.70377
“However, concerns have been raised regarding the limitations of DNA-based methods, specifically their inability to provide quantitative estimates of abundance (Elbrecht and Leese 2015; Lamb et al. 2019).”
Improving accessibility of species identification for wildlife crime prosecution: Expanding WildSEQ for calcified and keratinised materials
Yugovich, O., Cave, V., Sturrock, S., & Harbison, S. (2026) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2026.103524
Detecting terrestrial insects from naturally exuding tree sap using environmental DNA: a pilot studyPreprint
Kawakami, H., Yuasa, H., Kuroda, H., & Ichinose, T. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.16.724188
Drivers of soil invertebrate communities in a mining region as assessed by COI metabarcodingPreprint
Thomas, M., Martineau, C., Laganière, J., Porter, T. M., Morency, M., & Fenton, N. J. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.6876144
Predictors and consequences of diet composition in a declining generalist aerial insectivore
Uehling, J. J., Taff, C. C., Houtz, J. L., Becker, P. M., Injaian, A. S., & Vitousek, M. N. (2026) · Oecologia · doi:10.1007/s00442-026-05901-w
“…provides only a snapshot of what animals are eating within a day or two of sample collection (e.g., Thuo et al. 2019), and issues like primer bias (Elbrecht and Leese 2015 ) and differential digestion of DNA from different food sources through the digestive tract (Deagle and Tollit 2007) can lead…”
Unveiling the whale shark diet: Insights from stomach content DNA metabarcoding
Baciero, A. G., Loughlin, C. M., Ramírez‐Macías, D., & Munguía‐Vega, A. (2026) · Journal of Fish Biology · doi:10.1111/jfb.70534
NeMO : A Flexible R Package for Nested Multi‐Species Occupancy Modeling and eDNA Study Optimization
Macé, B., Manel, S., Valentini, A., Rocle, M., Roset, N., & Delrieu‐Trottin, E. (2026) · Environmental DNA · doi:10.1002/edn3.70326
TEMPORARY REMOVAL: Benthic eukaryotic biodiversity in submerged caves within subterranean estuaries of the Yucatan Peninsula and Cozumel Island, Mexico
Rohret, S. M., Calderón-Gutiérrez, F., Borda, E., Pohlman, J., Brankovits, D., Martínez, A., Mara, P., Edgcomb, V. P., & Bernhard, J. M. (2026) · Estuarine Coastal and Shelf Science · doi:10.1016/j.ecss.2026.110087
Retracted
Metabarcoding reveals scale-dependent diet breadth in disc-winged bats (Thyroptera tricolor)Preprint
Chaverri, G., Saltonstall, K., & Page, R. A. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7024338
Semi‐Quantitative Monitoring of Plant‐Arthropod Interactions by eDNA Metabarcoding of Individual Flowers and Leaves
Schmidt, A., Hank, J., Tello, M., Grevé, M. E., Baden, C. U., Maus, C., & Krehenwinkel, H. (2026) · Ecology and Evolution · doi:10.1002/ece3.73831
“As the method is based on PCR, amplification bias between different taxa in an arthropod community can lead to highly skewed abundance estimates (Elbrecht and Leese 2015; Fonseca 2018; Krehenwinkel et al. 2017).”
Dietary flexibility and high arthropod availability prevent food limitation in a mountain population of breeding Northern Wheatears
Mermillon, C., Chamberlain, D., Miquel, C., Coffie, D., Dumas, K., Rosselli, D., & Yannic, G. (2026) · Ibis · doi:10.1111/ibi.70090
Evaluation of two overlapping rbcL amplicons for routine diatom DNA biomonitoring
Pavla, U., & Štěpka, J. (2026) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.10.183921
“Mismatches in primer binding sites can reduce amplification efficiency and may lead to underrepresentation or failure to detect affected taxa (Elbrecht and Leese 2015; Piñol et al. 2015).”
Identifying the scale of effect of habitat for diversity and biomass of multiple arthropod taxa
Uhler, J., Kortmann, M., Mitesser, O., Zhang, J., Tobisch, C., Benjamin, C., Decker, O., Englmeier, J., Fricke, U., Ganuza, C., et al. (2026) · Landscape Ecology · doi:10.1007/s10980-026-02427-7
“Since a prior study demonstrated a strong positive correlation between specimen biomass and metabarcoding read abundance (Elbrecht and Leese 2015), we used these read percentages to partition each sample’s total biomass.”
Enabling Quantitative eDNA Monitoring in Lotic Ecosystems by Incorporating Hydrological Characteristics and Allometric Scaling
Driessche, C. V., Everts, T., Mauvisseau, Q., Neyrinck, S., Beer, B. D., Halfmaerten, D., Danneels, H., Bonte, D., & Brys, R. (2026) · Freshwater Biology · doi:10.1111/fwb.70308
A Pan‐European Whole‐Microbiome Study of Wastewater Influent: Prokaryotes, Protists, Fungi, and Metazoa
Nett, N., & Dumack, K. (2026) · Journal of Eukaryotic Microbiology · doi:10.1111/jeu.70112
“…biases (Mathieu-Daudé et al. 1996; Suzuki and Giovannoni 1996), primer mismatches due to the paraphyletic nature of protists (Martínez Rendón et al. 2025), as well as the use of different primer sets across studies, each favoring different taxa (Jeon et al. 2008; Elbrecht and Leese 2015).”
Getting to the Core of the Matter—Assessing the Role of Replication in Metabarcoding‐Based seda DNA
Baños, E., Segura, C. R., de Boer, E. J., Cundy, A. B., Turón, X., Nogué, S., Holman, L. E., & Rius, M. (2026) · Molecular Ecology Resources · doi:10.1111/1755-0998.70200
“…these metabarcoding-based seda DNA studies are particularly useful for comparative ecological analyses, although their interpretation should acknowledge limitations associated with PCR amplification biases and differential DNA preservation (Elbrecht and Leese 2015; Shaffer et al. 2025).”
Plant and fungal eDNA metabarcoding for geographic sourcing of forensic palynological evidence across urban functional zones
Ma, H., Ningrui, X. U., Zhen, X., Liu, J., Xun, X., & Lai, J. (2026) · Forensic Science International · doi:10.1016/j.forsciint.2026.113135
Fish Community Composition Revealed by eDNA Metabarcoding in Mangrove‐Associated Lagoons of Negombo and Puttalam, Sri Lanka
Priyadarshika, T., Juliano, M. G., Hirimuthugoda, N. Y., PANANGANAN, B. G. S., Isowa, Y., Liyanagedara, P., Ranawana, K. B., Chu, C., Kajita, T., & Kumburegama, S. (2026) · Environmental DNA · doi:10.1002/edn3.70362
Comparison of eDNA, bulk-community metabarcoding, and morphological identification approaches for assessing stream macroinvertebrate communities
Doloiras-Laraño, A. D., Yaegashi, S., Serrana, J. M., Ishitani, N., & Watanabe, K. (2026) · Ecological Indicators · doi:10.1016/j.ecolind.2026.115390
Complementary but Not Interchangeable: A Comparison of eDNA and Bulk Sample Metabarcoding for the Assessment of Groundwater Invertebrate Communities
Rau, H., Hoeschel, T., Hahn, H. J., & Schwenk, K. (2026) · Environmental DNA · doi:10.1002/edn3.70366
Novel 12S/16S rRNA markers for quantitative metabarcoding of mammalian mixtures
Yu, P., Wang, C., Liu, Y., Xu, Z., Sun, Q., & Zhang, W. (2026) · Food Control · doi:10.1016/j.foodcont.2026.112630
Beyond cichlid diversification: environmental drivers of biodiversity across the Nicaraguan lake system
Agudo, J. C., Leal‐Cardín, M., Riesgo, A., Gallego, R., & Barluenga, M. (2026) · Hydrobiologia · doi:10.1007/s10750-026-06401-x
On the effectiveness of two universal metabarcoding primer pairs in amplifying Arctic gelatinous zooplankton DNA from tissue and environmental samples
Murray, A., Dischereit, A., & Havermans, C. (2026) · Frontiers in Marine Science · doi:10.3389/fmars.2026.1875281
Gut microbiomes of the little free-tailed bat ( Mops pumilus ) show high prevalence of potential bacterial pathogens but limited responses to land cover
Shapiro, J. T., Barnes, C., Nielsen, I. B., Rasmussen, L., Monadjem, A., McCleery, R. A., & Hansen, A. J. (2026) · Web Ecology · doi:10.5194/we-26-223-2026
Knowledge-guided taxon selection aligns eDNA with morphology-based diatom indices
Kim, T., Kim, H., Muhammad, B. L., & Ki, J. (2026) · Environmental Science and Ecotechnology · doi:10.1016/j.ese.2026.100779
“If the abundance of a specific species artificially explodes due to PCR bias, its influence on the model can expand limitlessly [46].”
Combining Morpho‐Taxonomy and Metabarcoding Enhances the Detection of Biofouling Communities at Offshore Sites
Portas, A., Pinsivy, L., Grall, J., Damblans, G., Briand, J., & Quillien, N. (2026) · Environmental DNA · doi:10.1002/edn3.70378
From Ecological States to Trajectories: Revealing Ecological Dynamics Through Environmental Nucleic Acids
Xiong, W., & Zhan, A. (2026) · Biological Diversity · doi:10.1002/bod2.70040
The Known Unknowns: Identifying and bridging information gaps in European freshwater invertebrate biodiversity to inform conservation effortsPreprint
Kelly‐Quinn, M., Jones, J. I., Fontaneto, D., Stubbington, R., Boda, P., Boix, D., Erba, S., Külköylüoğlu, O., Rasmussen, J. J., Sandin, L., et al. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7664901
Environmental DNA-derived indicators reveal species turnover and connectivity-related ecological patterns across patch-corridor-matrix framework
Zuzolo, D., Creer, S., Ellison, A., Tartaglia, M., Prigioniero, A., Ranauda, M. A., Maisto, M., Gizzi, G., Scarano, P., Labella-Ortega, M., et al. (2026) · Ecological Indicators · doi:10.1016/j.ecolind.2026.115748
Challenges of soil arthropod community assessments: Large site-related variation and hidden species-level diversity
Fernández‐Bravo, M., Gschwend, F., Mayerhofer, J., Moll, J., Widmer, F., & Enkerli, J. (2026) · Applied Soil Ecology · doi:10.1016/j.apsoil.2026.107549

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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