water Review Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates Sofia Duarte 1,2,*, Barbara R. Leite 1,2 , Maria João Feio 3 , Filipe O. Costa 1,2 and Ana Filipa Filipe 4,5 1 Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
[email protected] (B.R.L.);
[email protected] (F.O.C.) 2 Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal 3 Department of Life Sciences, MARE-Marine and Environmental Sciences Centre, University of Coimbra, 3000-456 Coimbra, Portugal;
[email protected] 4 School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisboa, Portugal; affi
[email protected] 5 CIBIO/InBIO—Research Centre in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, 4485-661 Vairão, Portugal * Correspondence:
[email protected] Abstract: Benthic macroinvertebrates are among the most used biological quality elements for assess- ing 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 Citation: Duarte, S.; Leite, B.R.; Feio, artificial structures has been favored.