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Review

Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

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Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Department of Life Sciences, MARE-Marine and Environmental Sciences Centre, University of Coimbra, 3000-456 Coimbra, Portugal
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School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisboa, Portugal
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CIBIO/InBIO—Research Centre in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, 4485-661 Vairão, Portugal
*
Author to whom correspondence should be addressed.
Academic Editor: H. Jan Janse
Water 2021, 13(3), 331; https://doi.org/10.3390/w13030331
Received: 21 December 2020 / Revised: 19 January 2021 / Accepted: 25 January 2021 / Published: 29 January 2021
(This article belongs to the Special Issue The Ecological Assessment of Rivers and Estuaries: Present and Future)
Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs. View Full-Text
Keywords: aquatic ecosystems; biomonitoring; bioassessment; benthic macroinvertebrates; DNA metabarcoding aquatic ecosystems; biomonitoring; bioassessment; benthic macroinvertebrates; DNA metabarcoding
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MDPI and ACS Style

Duarte, S.; Leite, B.R.; Feio, M.J.; Costa, F.O.; Filipe, A.F. Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. Water 2021, 13, 331. https://doi.org/10.3390/w13030331

AMA Style

Duarte S, Leite BR, Feio MJ, Costa FO, Filipe AF. Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. Water. 2021; 13(3):331. https://doi.org/10.3390/w13030331

Chicago/Turabian Style

Duarte, Sofia, Barbara R. Leite, Maria J. Feio, Filipe O. Costa, and Ana F. Filipe. 2021. "Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates" Water 13, no. 3: 331. https://doi.org/10.3390/w13030331

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