Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate seq...
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| Veröffentlicht in: | Molecular ecology Jg. 26; H. 21; S. 5872 - 5895 |
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| Hauptverfasser: | , , , , , , , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
England
Blackwell Publishing Ltd
01.11.2017
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| Schlagworte: | |
| ISSN: | 0962-1083, 1365-294X, 1365-294X |
| Online-Zugang: | Volltext |
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| Abstract | The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education. |
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| AbstractList | The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“
HTS
”) platforms now enable the rapid sequencing of
DNA
from diverse kinds of environmental samples (termed “environmental
DNA
” or “
eDNA
”). Coupling
HTS
with our ability to associate sequences from
eDNA
with a taxonomic name is called “
eDNA
metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of
eDNA
metabarcoding for surveying animal and plant richness, and the challenges in using
eDNA
approaches to estimate relative abundance. We highlight
eDNA
applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different
eDNA
sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the
eDNA
metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of
eDNA
metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how
eDNA
metabarcoding can empower citizen science and biodiversity education. The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education. The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education. |
| Author | Bik, Holly M. Seymour, Mathew Lacoursière‐Roussel, Anaïs Deiner, Kristy Altermatt, Florian Mächler, Elvira Vere, Natasha Bernatchez, Louis Creer, Simon Pfrender, Michael E. Lodge, David M. Bista, Iliana |
| Author_xml | – sequence: 1 givenname: Kristy orcidid: 0000-0001-9755-3223 surname: Deiner fullname: Deiner, Kristy email: alpinedna@gmail.com organization: Cornell University – sequence: 2 givenname: Holly M. orcidid: 0000-0002-4356-3837 surname: Bik fullname: Bik, Holly M. organization: University of California – sequence: 3 givenname: Elvira surname: Mächler fullname: Mächler, Elvira organization: University of Zurich – sequence: 4 givenname: Mathew surname: Seymour fullname: Seymour, Mathew organization: Bangor University – sequence: 5 givenname: Anaïs orcidid: 0000-0002-9345-5682 surname: Lacoursière‐Roussel fullname: Lacoursière‐Roussel, Anaïs organization: Université Laval – sequence: 6 givenname: Florian orcidid: 0000-0002-4831-6958 surname: Altermatt fullname: Altermatt, Florian organization: University of Zurich – sequence: 7 givenname: Simon orcidid: 0000-0003-3124-3550 surname: Creer fullname: Creer, Simon organization: Bangor University – sequence: 8 givenname: Iliana surname: Bista fullname: Bista, Iliana organization: Wellcome Trust Sanger Institute – sequence: 9 givenname: David M. surname: Lodge fullname: Lodge, David M. organization: Cornell University – sequence: 10 givenname: Natasha orcidid: 0000-0001-9593-6925 surname: Vere fullname: Vere, Natasha organization: Aberystwyth University – sequence: 11 givenname: Michael E. surname: Pfrender fullname: Pfrender, Michael E. organization: University of Notre Dame – sequence: 12 givenname: Louis surname: Bernatchez fullname: Bernatchez, Louis organization: Université Laval |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28921802$$D View this record in MEDLINE/PubMed |
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| Snippet | The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid... The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“ HTS ”) platforms now enable the rapid... The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid... |
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| SubjectTerms | Animals Biodiversity bioinformatic pipeline bioinformatics Biomonitoring citizen science conservation Conservation of Natural Resources Coupling (molecular) data collection Deoxyribonucleic acid DNA DNA barcoding DNA Barcoding, Taxonomic - methods DNA Primers DNA sequencing ecology Ecology - methods ecosystems eDNA education Environmental DNA Environmental Monitoring experimental design Filtration freshwater high-throughput nucleotide sequencing invasive species macro‐organism Nucleotide sequence Plant communities Plants Primers Relative abundance species diversity Species richness Surveying surveys Terrestrial environments Workflow |
| Title | Environmental DNA metabarcoding: Transforming how we survey animal and plant communities |
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