Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Zimmermann, Jonas; Glöckner, Gernot; Jahn, Regine; Enke, Neela; Gemeinholzer, Birgit

doi:10.1111/1755-0998.12336

Cited by 323Environmental DNA in Biodiversity StudiesMicrobial Community Ecology and PhysiologyDiatoms and Algae Research

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Zimmermann, Jonas, Glöckner, Gernot, Jahn, Regine, Enke, Neela, Gemeinholzer, Birgit·2015·Molecular Ecology Resources

DOI 10.1111/1755-0998.12336

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Abstract

Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time‐consuming and needs in‐depth knowledge of the organisms under investigation, as nonhomoplastic species‐specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence‐based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA‐based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy.

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Several studies show that DNA-based assessments are superior to morphological assessments in freshwater ecosystems.
“Several studies show that DNA-based assessments are superior to morphological assessments in freshwater ecosystems (e.g., [14,25,33])”
From Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol (2015) · cites this paper as [33]

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First Evidence of the Existence of Semi-Cryptic Species and of a Phylogeographic Structure in the Gomphonema parvulum (Kützing) Kützing Complex (Bacillariophyta)
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Self-citation
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA
Ruppert, K. M., Kline, R. J., & Rahman, M. S. (2019) · Global Ecology and Conservation · doi:10.1016/j.gecco.2019.e00547 · Cited by 1,258 · see citing works
Environmental DNA
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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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Environmental DNA reveals that rivers are conveyer belts of biodiversity information
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DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work
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The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
Pawlowski, J. W., Kelly‐Quinn, M., Altermatt, F., Apothéloz‐Perret‐Gentil, L., Beja, P. R., Boggero, A., Borja, Á., Bouchez, A., Cordier, T., Domaizon, I., et al. (2018) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2018.05.002 · Cited by 562 · see citing works
Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive
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Assessing strengths and weaknesses of DNA metabarcoding‐based macroinvertebrate identification for routine stream monitoring
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Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site
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Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment
Aylagas, E., Borja, Á., Irigoien, X., & Rodríguez‐Ezpeleta, N. (2016) · Frontiers in Marine Science · doi:10.3389/fmars.2016.00096 · Cited by 262 · see citing works
Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment
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Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons
Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, É., Wangensteen, O. S., & Turón, X. (2015) · PLoS ONE · doi:10.1371/journal.pone.0139633 · Cited by 255 · see citing works
High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems
Lejzerowicz, F., Esling, P., Pillet, L., Wilding, T. A., Black, K., & Pawlowski, J. W. (2015) · Scientific Reports · doi:10.1038/srep13932 · Cited by 254 · see citing works
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods
Pawlowski, J. W., Bruce, K., Panksep, K., Aguirre, F. I., Amalfitano, S., Apothéloz‐Perret‐Gentil, L., Baussant, T., Bouchez, A., Carugati, L., Cermakova, K., et al. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.151783 · Cited by 232 · see citing works
Expanding Ecological Assessment by Integrating Microorganisms into Routine Freshwater Biomonitoring
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Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data
Visco, J. A., Apothéloz‐Perret‐Gentil, L., Cordonier, A., Esling, P., Pillet, L., & Pawlowski, J. W. (2015) · Environmental Science & Technology · doi:10.1021/es506158m · Cited by 225 · see citing works
Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning
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Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France)
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Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples
Lear, G., Dickie, I. A., Banks, J. C., Boyer, S., Buckley, H. L., Buckley, T. R., Cruickshank, R., Dopheide, A., Handley, K. M., Hermans, S. M., et al. (2018) · New Zealand Journal of Ecology · doi:10.20417/nzjecol.42.9 · Cited by 181 · see citing works
Diat.barcode, an open-access curated barcode library for diatoms
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Self-citation
Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring
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Protist metabarcoding and environmental biomonitoring: Time for change
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Supervised machine learning outperforms taxonomy‐based environmental DNA metabarcoding applied to biomonitoring
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Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks
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Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA
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Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action
Leese, F., Bouchez, A., Abarenkov, K., Altermatt, F., Borja, Á., Bruce, K., Ekrem, T., ČIAMPOR, F. J., Čiamporová‐Zaťovičová, Z., Costa, F. O., et al. (2018) · Advances in ecological research/Advances in Ecological Research · doi:10.1016/bs.aecr.2018.01.001 · Cited by 151 · see citing works
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Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring
Vasselon, V., Bouchez, A., Rimet, F., Jacquet, S., Trobajo, R., Corniquel, M., Tapolczai, K., & Domaizon, I. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12960 · Cited by 150 · see citing works
Diatoms as Bioindicators in Rivers
Lobo, E. A., Heinrich, C. G., Schuch, M., Wetzel, C. E., & Éctor, L. (2016) · Springer eBooks · doi:10.1007/978-3-319-31984-1_11 · Cited by 149 · see citing works
Comparison of environmental DNA and bulk‐sample metabarcoding using highly degenerate cytochrome c oxidase I primers
Macher, J., Vivancos, A., Piggott, J. J., Centeno, F. C., Matthaei, C. D., & Leese, F. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12940 · Cited by 136 · see citing works
Towards a multisensor station for automated biodiversity monitoring
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Self-citation
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Goodwin, K. D., Thompson, L., Duarte, B., Kahlke, T., Thompson, A. R., Marques, J. C., & Caçador, I. (2017) · Frontiers in Marine Science · doi:10.3389/fmars.2017.00107 · Cited by 124 · see citing works
Taxonomic Reference Libraries for Environmental Barcoding: A Best Practice Example from Diatom Research
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Self-citation
A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations
Laroche, O., Wood, S. A., Tremblay, L. A., Ellis, J. I., Lear, G., & Pochon, X. (2017) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2017.11.042 · Cited by 119 · see citing works
Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?
Vasselon, V., Domaizon, I., Rimet, F., Kahlert, M., & Bouchez, A. (2017) · Freshwater Science · doi:10.1086/690649 · Cited by 117 · see citing works
Automatic image‐based identification and biomass estimation of invertebrates
Ärje, J., Melvad, C., Jeppesen, M. R., Madsen, S. A., Raitoharju, J., Rasmussen, M. S., Iosifidis, A., Tirronen, V., Gabbouj, M., Meissner, K. K., et al. (2020) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13428 · Cited by 115 · see citing works
Ecogenomics of Zooplankton Community Reveals Ecological Threshold of Ammonia Nitrogen
Yang, J., Zhang, X., Xie, Y., Song, C., Sun, J., Zhang, Y., Giesy, J. P., & Yu, H. (2017) · Environmental Science & Technology · doi:10.1021/acs.est.6b05606 · Cited by 114 · see citing works
Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports
Chain, F. J. J., Brown, E. A., MacIsaac, H. J., & Cristescu, M. E. (2016) · Diversity and Distributions · doi:10.1111/ddi.12427 · Cited by 113 · see citing works
Morphology, typification and critical analysis of some ecologically important small naviculoid species (Bacillariophyta)
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High‐throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil‐drilling activities
Lanzén, A., Lekang, K., Jonassen, I., Thompson, E. M., & Troedsson, C. (2016) · Molecular Ecology · doi:10.1111/mec.13761 · Cited by 104 · see citing works
Molecular biogeography of planktonic and benthic diatoms in the Yangtze River
Wang, J., Liu, Q., Zhao, X., Borthwick, A. G. L., Liu, Y., Chen, Q., & Ni, J. (2019) · Microbiome · doi:10.1186/s40168-019-0771-x · Cited by 104 · see citing works
Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics
Vitecek, S., Kučinić, M., Previšić, A., Živić, I. M., Stojanović, K. Z., Keresztes, L., Bálint, M., Hoppeler, F., Waringer, J. A., Graf, W., et al. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0972-5 · Cited by 97 · see citing works
Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment
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Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization
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Self-citation
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring
Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., Franc, A., & Bouchez, A. (2016) · Database · doi:10.1093/database/baw016 · Cited by 94 · see citing works
Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities
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Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index
Apothéloz‐Perret‐Gentil, L., Bouchez, A., Cordier, T., Cordonier, A., Guéguen, J., Rimet, F., Vasselon, V., & Pawlowski, J. W. (2020) · Molecular Ecology · doi:10.1111/mec.15646 · Cited by 91 · see citing works
Diet Assessment Based on Rumen Contents: A Comparison between DNA Metabarcoding and Macroscopy
Nichols, R. V., Åkesson, M., & Kjellander, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157977 · Cited by 90 · see citing works
Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring in salmon aquaculture
Stoeck, T., Kochems, R., Forster, D., Lejzerowicz, F., & Pawlowski, J. W. (2017) · Ecological Indicators · doi:10.1016/j.ecolind.2017.10.041 · Cited by 90 · see citing works
Benthic algae assessments in the EU and the US: Striving for consistency in the face of great ecological diversity
Charles, D. F., KELLY, M. G., Stevenson, R. J., Poikāne, S., Theroux, S. M., Zgrundo, A., & Cantonati, M. (2020) · Ecological Indicators · doi:10.1016/j.ecolind.2020.107082 · Cited by 88 · see citing works
Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring
Serrana, J. M., Miyake, Y., Gamboa, M., & Watanabe, K. (2019) · Ecological Indicators · doi:10.1016/j.ecolind.2019.02.008 · Cited by 81 · see citing works
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status
Bailet, B., Bouchez, A., Franc, A., Frigerio, J.-M., Keck, F., Karjalainen, S. M., Rimet, F., Schneider, S. C., & Kahlert, M. (2019) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.3.34002 · Cited by 77 · see citing works
Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms
Mortágua, A., Vasselon, V., de Oliveira, R. A. C., Elias, C. L., Chardon, C., Bouchez, A., Rimet, F., Feio, M. J., & Almeida, S. F. P. (2019) · Ecological Indicators · doi:10.1016/j.ecolind.2019.105470 · Cited by 74 · see citing works
Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding
Pawlowski, J. W., Esling, P., Lejzerowicz, F., Cordier, T., Visco, J. A., Martins, C., Kvalvik, A., Staven, K., & Cedhagen, T. (2016) · Aquaculture Environment Interactions · doi:10.3354/aei00182 · Cited by 72 · see citing works
The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods
Groendahl, S., Kahlert, M., & Fink, P. (2017) · PLoS ONE · doi:10.1371/journal.pone.0172808 · Cited by 72 · see citing works
Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities
von Ammon, U., Wood, S. A., Laroche, O., Zaiko, A., Tait, L. W., Lavery, S., Inglis, G. J., & Pochon, X. (2018) · Scientific Reports · doi:10.1038/s41598-018-34541-1 · Cited by 72 · see citing works
A simple 18S rDNA approach for the identification of cultured eukaryotic microalgae with an emphasis on primers
Khaw, Y. S., Khong, N. M. H., Shaharuddin, N. A., & Yusoff, F. M. (2020) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2020.105890 · Cited by 71 · see citing works
Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles
Keck, F., Vasselon, V., Rimet, F., Bouchez, A., & Kahlert, M. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12919 · Cited by 70 · see citing works
Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software
Rivera, S. F., Vasselon, V., Bouchez, A., & Rimet, F. (2019) · Ecological Indicators · doi:10.1016/j.ecolind.2019.105775 · Cited by 67 · see citing works
Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
Rimet, F., Vasselon, V., A.-Keszte, B., & Bouchez, A. (2018) · Organisms Diversity & Evolution · doi:10.1007/s13127-018-0359-5 · Cited by 67 · see citing works
Diatom diversity through HTS-metabarcoding in coastal European seas
Piredda, R., Claverie, J., Decelle, J., de Vargas, C., Dunthorn, M., Edvardsen, B., Eikrem, W., Forster, D., Kooistra, W. H. C. F., Logares, R., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-36345-9 · Cited by 67 · see citing works
Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences
Marques, V., Guérin, P., Rocle, M., Valentini, A., Manel, S., Mouillot, D., & Déjean, T. (2020) · Ecography · doi:10.1111/ecog.05049 · Cited by 65 · see citing works
Metabarcoding unsorted kick‐samples facilitates macroinvertebrate‐based biomonitoring with increased taxonomic resolution, while outperforming environmental DNA
da Conceicoa, L. P., Elbrecht, V., Hall, A. C., Briscoe, A. G., Barber‐James, H. M., & Price, B. W. (2020) · Environmental DNA · doi:10.1002/edn3.116 · Cited by 65 · see citing works
Development of a novel metric for evaluating diatom assemblages in rivers using DNA metabarcoding
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Data from: Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies
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Diatoms as Bioindicators : A Molecular Approach
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Vasselon, V., Rimet, F., Domaizon, I., Monnier, O., Reyjol, Y., & Bouchez, A. (2019) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.3.39646 · Cited by 56 · see citing works
Benthic diatom eDNA metabarcoding for ecological assessment of an urban river: A comparison with morphological method
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A bibliometric study on diatom DNA metabarcording for water quality monitoring: a global perspective
Mbao, E. O., Nyika, J. M., Sheng, T., Ochieng, B., Sitoki, L. M., Oduor, S. O., Kitaka, N. K., Olaka, L. A., & Tan, C. (2023) · African Journal of Aquatic Science · doi:10.2989/16085914.2023.2282493 · Cited by 8 · see citing works

Authors: Zimmermann, J., Glöckner, G., Jahn, R., Enke, N., & Gemeinholzer, B.
Affiliations: Justus-Liebig-Universität Gießen (DE)
University of Cologne (DE)
Botanic Garden and Botanical Museum Berlin (DE)
Corresponding author: Zimmermann, Jonas
ORCID: Zimmermann, Jonas
Glöckner, Gernot
Jahn, Regine
Gemeinholzer, Birgit
Venue: Molecular Ecology Resources
Publisher: Wiley
Published: 2014-10-20
Volume: 15
Issue: 3
Pages: 526-542
ISSN: 1755-098X (ISSN-L)
1755-0998
DOI: 10.1111/1755-0998.12336
OpenAlex: W2089848025
Cited by: 317
References: 101
Citations by year: 2026: 17 · 2025: 23 · 2024: 39 · 2023: 24 · 2022: 21 · 2021: 23 · 2020: 41 · 2019: 26 · 2018: 55 · 2017: 25 · 2016: 14 · 2015: 7 · 2014: 1
FWCI: 13.58
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Molecular Ecology Resources (publishedVersion)
PubMed (publishedVersion)
Funders: Deutsche Forschungsgemeinschaft (GE 12 42/11-1)
Topics: Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Physical Sciences › Materials Science › Biomaterials › Diatoms and Algae Research
Keywords: diatoms, metabarcoding, morphological identification, species identification, water quality assessment, reference database, rare taxa, Oder River
MeSH terms: Algorithms, Cytological Techniques, Fresh Water, Microscopy, Molecular Sequence Data, Genetic Variation, Diatoms, Sequence Analysis, DNA, Biodiversity, Rivers, Workflow, DNA Barcoding, Taxonomic, Water Quality

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Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

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