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

  • SCI-E
作者: Duarte, Sofia;Leite, Barbara R.;Feio, Maria Joao;Costa, Filipe O.;Filipe, Ana Filipa
作者机构: Department of Life Sciences, MARE-Marine and Environmental Sciences Centre, University of Coimbra, 3000-456 Coimbra, Portugal
CIBIO/InBIO—Research Centre in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, 4485-661 Vairão, Portugal
School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisboa, Portugal
Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
语种: 英文
关键词: aquatic ecosystems;biomonitoring;bioassessment;benthic macroinvertebrates;DNA metabarcoding
期刊: Water
年: 2021
卷: 13
期: 3
页码: 331
基金类别: "Contrato-Programa" - national funds through the FCT I.P (Foundation for Science and Technology) [UIDB/04050/2020]; project NIS-DNA - national funds through the FCT I.P (Foundation for Science and Technology); FCTPortuguese Foundation for Science and TechnologyEuropean Commission [CEECIND/00667/2017, PD/BD/127994/2016]; project FRESHING - FCT; COMPETE [PTDC/AAGMAA/2261/2014-POCI-01-0145-FEDER356016824]; FCT through MARE strategic project [UIDB/04292/2020]; Norma Transitoria [DL57/2016]
摘要: 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.

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