Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates
An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but t...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2019-11-01
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| Series: | Frontiers in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fevo.2019.00434/full |
| _version_ | 1818322878712512512 |
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| author | Alex Bush Zacchaeus G. Compson Wendy A. Monk Wendy A. Monk Teresita M. Porter Teresita M. Porter Royce Steeves Erik Emilson Nellie Gagne Mehrdad Hajibabaei Mélanie Roy Donald J. Baird |
| author_facet | Alex Bush Zacchaeus G. Compson Wendy A. Monk Wendy A. Monk Teresita M. Porter Teresita M. Porter Royce Steeves Erik Emilson Nellie Gagne Mehrdad Hajibabaei Mélanie Roy Donald J. Baird |
| author_sort | Alex Bush |
| collection | DOAJ |
| description | An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a biodiversity observation tool provides a potential solution. As high-throughput sequencing becomes more rapid and cost-effective, a “big data” revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater sample processing capacity. These advances have the potential to amplify the power of ecological studies to detect change and diagnose its cause, through a methodology termed “Biomonitoring 2.0.” Despite its promise, the unfamiliar terminology and pace of development in high-throughput sequencing technologies has contributed to a growing concern that an unproven technology is supplanting tried and tested approaches, lowering trust among potential users, and reducing uptake by ecologists and environmental management practitioners. While it is reasonable to exercise caution, we argue that any criticism of new methods must also acknowledge the shortcomings and lower capacity of current observation methods. Broader understanding of the statistical properties of metabarcoding data will help ecologists to design, test and review evidence for new hypotheses. We highlight the uncertainties and challenges underlying DNA metabarcoding and traditional methods for compositional analysis, specifically comparing the interpretation of otherwise identical bulk-community samples of freshwater benthic invertebrates. We explore how taxonomic resolution, sample similarity, taxon misidentification, and taxon abundance affect the statistical properties of these samples, but recognize these issues are relevant to applications across all ecosystem types. In conclusion, metabarcoding has the capacity to improve the quality and utility of ecological data, and consequently the quality of new research and efficacy of management responses. |
| first_indexed | 2024-12-13T11:03:48Z |
| format | Article |
| id | doaj.art-b817698d9bc44559a74caca5b5e8316e |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-12-13T11:03:48Z |
| publishDate | 2019-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-b817698d9bc44559a74caca5b5e8316e2022-12-21T23:49:09ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2019-11-01710.3389/fevo.2019.00434484625Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic MacroinvertebratesAlex Bush0Zacchaeus G. Compson1Wendy A. Monk2Wendy A. Monk3Teresita M. Porter4Teresita M. Porter5Royce Steeves6Erik Emilson7Nellie Gagne8Mehrdad Hajibabaei9Mélanie Roy10Donald J. Baird11Department of Biology, Environment and Climate Change Canada, Canadian Rivers Institute, University of New Brunswick, Fredericton, NB, CanadaDepartment of Biology, Environment and Climate Change Canada, Canadian Rivers Institute, University of New Brunswick, Fredericton, NB, CanadaDepartment of Biology, Environment and Climate Change Canada, Canadian Rivers Institute, University of New Brunswick, Fredericton, NB, CanadaFaculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, CanadaGreat Lakes Forestry Centre, Natural Resources Canada, Marie, ON, CanadaCentre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, CanadaDepartment for Fisheries and Oceans, Gulf Fisheries Centre, Moncton, NB, CanadaGreat Lakes Forestry Centre, Natural Resources Canada, Marie, ON, CanadaDepartment for Fisheries and Oceans, Gulf Fisheries Centre, Moncton, NB, CanadaCentre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, CanadaDepartment for Fisheries and Oceans, Gulf Fisheries Centre, Moncton, NB, CanadaDepartment of Biology, Environment and Climate Change Canada, Canadian Rivers Institute, University of New Brunswick, Fredericton, NB, CanadaAn ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a biodiversity observation tool provides a potential solution. As high-throughput sequencing becomes more rapid and cost-effective, a “big data” revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater sample processing capacity. These advances have the potential to amplify the power of ecological studies to detect change and diagnose its cause, through a methodology termed “Biomonitoring 2.0.” Despite its promise, the unfamiliar terminology and pace of development in high-throughput sequencing technologies has contributed to a growing concern that an unproven technology is supplanting tried and tested approaches, lowering trust among potential users, and reducing uptake by ecologists and environmental management practitioners. While it is reasonable to exercise caution, we argue that any criticism of new methods must also acknowledge the shortcomings and lower capacity of current observation methods. Broader understanding of the statistical properties of metabarcoding data will help ecologists to design, test and review evidence for new hypotheses. We highlight the uncertainties and challenges underlying DNA metabarcoding and traditional methods for compositional analysis, specifically comparing the interpretation of otherwise identical bulk-community samples of freshwater benthic invertebrates. We explore how taxonomic resolution, sample similarity, taxon misidentification, and taxon abundance affect the statistical properties of these samples, but recognize these issues are relevant to applications across all ecosystem types. In conclusion, metabarcoding has the capacity to improve the quality and utility of ecological data, and consequently the quality of new research and efficacy of management responses.https://www.frontiersin.org/article/10.3389/fevo.2019.00434/fullbiodiversity observationhigh-throughput sequencingtaxonomic resolutioncommunity ecologyenvironmental genomicsfreshwater |
| spellingShingle | Alex Bush Zacchaeus G. Compson Wendy A. Monk Wendy A. Monk Teresita M. Porter Teresita M. Porter Royce Steeves Erik Emilson Nellie Gagne Mehrdad Hajibabaei Mélanie Roy Donald J. Baird Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates Frontiers in Ecology and Evolution biodiversity observation high-throughput sequencing taxonomic resolution community ecology environmental genomics freshwater |
| title | Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates |
| title_full | Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates |
| title_fullStr | Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates |
| title_full_unstemmed | Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates |
| title_short | Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates |
| title_sort | studying ecosystems with dna metabarcoding lessons from biomonitoring of aquatic macroinvertebrates |
| topic | biodiversity observation high-throughput sequencing taxonomic resolution community ecology environmental genomics freshwater |
| url | https://www.frontiersin.org/article/10.3389/fevo.2019.00434/full |
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