Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of...

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Veröffentlicht in:Molecular ecology Jg. 31; H. 6; S. 1820 - 1835
Hauptverfasser: Keck, François, Blackman, Rosetta C., Bossart, Raphael, Brantschen, Jeanine, Couton, Marjorie, Hürlemann, Samuel, Kirschner, Dominik, Locher, Nadine, Zhang, Heng, Altermatt, Florian
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Blackwell Publishing Ltd 01.03.2022
John Wiley and Sons Inc
Schlagworte:
Aquatic communities
Aquatic organisms
Biodiversity
Community structure
Complementarity
Data collection
Deoxyribonucleic acid
diversity assessment
DNA
DNA barcoding
Environmental DNA
Estimates
Fish
freshwater
Inventories
invertebrates
Macroinvertebrates
Meta-analysis
metabarcoding
microorganisms
Original
ORIGINAL ARTICLES
Plankton
diversity assessment
metabarcoding
microorganisms
DNA
fish
meta-analysis
invertebrates
ISSN:0962-1083, 1365-294X, 1365-294X
Online-Zugang:Volltext
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Abstract DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
AbstractList DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho-taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA-based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta-analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho-taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA-based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta-analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
Author Kirschner, Dominik
Hürlemann, Samuel
Blackman, Rosetta C.
Altermatt, Florian
Bossart, Raphael
Couton, Marjorie
Locher, Nadine
Keck, François
Zhang, Heng
Brantschen, Jeanine
AuthorAffiliation 3 27217 Research Priority Programme Global Change and Biodiversity (URPP‐GCB) University of Zurich Zürich Switzerland
4 Landscape Ecology Institute of Terrestrial Ecosystems Department of Environmental System Science ETH Zürich Zürich Switzerland
5 Landscape Ecology, Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
1 Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
2 27217 Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
AuthorAffiliation_xml – name: 3 27217 Research Priority Programme Global Change and Biodiversity (URPP‐GCB) University of Zurich Zürich Switzerland
– name: 4 Landscape Ecology Institute of Terrestrial Ecosystems Department of Environmental System Science ETH Zürich Zürich Switzerland
– name: 1 Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
– name: 2 27217 Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
– name: 5 Landscape Ecology, Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
Author_xml – sequence: 1
  givenname: François
  orcidid: 0000-0002-3323-4167
  surname: Keck
  fullname: Keck, François
  email: francois.keck@gmail.com
  organization: Eawag: Swiss Federal Institute of Aquatic Science and Technology
– sequence: 2
  givenname: Rosetta C.
  orcidid: 0000-0002-6182-8691
  surname: Blackman
  fullname: Blackman, Rosetta C.
  organization: University of Zurich
– sequence: 3
  givenname: Raphael
  surname: Bossart
  fullname: Bossart, Raphael
  organization: Eawag: Swiss Federal Institute of Aquatic Science and Technology
– sequence: 4
  givenname: Jeanine
  orcidid: 0000-0002-2945-3607
  surname: Brantschen
  fullname: Brantschen, Jeanine
  organization: University of Zurich
– sequence: 5
  givenname: Marjorie
  orcidid: 0000-0001-9880-8646
  surname: Couton
  fullname: Couton, Marjorie
  organization: Eawag: Swiss Federal Institute of Aquatic Science and Technology
– sequence: 6
  givenname: Samuel
  surname: Hürlemann
  fullname: Hürlemann, Samuel
  organization: Eawag: Swiss Federal Institute of Aquatic Science and Technology
– sequence: 7
  givenname: Dominik
  orcidid: 0000-0001-5592-0494
  surname: Kirschner
  fullname: Kirschner, Dominik
  organization: Swiss Federal Institute for Forest, Snow and Landscape Research WSL
– sequence: 8
  givenname: Nadine
  surname: Locher
  fullname: Locher, Nadine
  organization: Eawag: Swiss Federal Institute of Aquatic Science and Technology
– sequence: 9
  givenname: Heng
  orcidid: 0000-0002-3139-9566
  surname: Zhang
  fullname: Zhang, Heng
  organization: University of Zurich
– sequence: 10
  givenname: Florian
  orcidid: 0000-0002-4831-6958
  surname: Altermatt
  fullname: Altermatt, Florian
  email: florian.altermatt@eawag.ch
  organization: University of Zurich
BackLink https://www.ncbi.nlm.nih.gov/pubmed/35075700$$D View this record in MEDLINE/PubMed
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Copyright 2022 The Authors. published by John Wiley & Sons Ltd.
2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.
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Issue 6
Keywords diversity assessment
metabarcoding
microorganisms
DNA
fish
meta-analysis
invertebrates
Language English
License Attribution
2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.
This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Notes François Keck and Rosetta Blackman are joint first authors.
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Snippet DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with...
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wiley
SourceType Open Access Repository
Aggregation Database
Index Database
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StartPage 1820
SubjectTerms Aquatic communities
Aquatic organisms
Biodiversity
Community structure
Complementarity
Data collection
Deoxyribonucleic acid
diversity assessment
DNA
DNA barcoding
Environmental DNA
Estimates
Fish
freshwater
Inventories
invertebrates
Macroinvertebrates
Meta-analysis
metabarcoding
microorganisms
Original
ORIGINAL ARTICLES
Plankton
Title Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fmec.16364
https://www.ncbi.nlm.nih.gov/pubmed/35075700
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Volume 31
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