Abstract
Simple SummaryThe biodiversity and ecological status assessment of transitional water ecosystems by benthic macroinvertebrates investigation could use DNA barcode tools for more rapid and efficient outputs. The principal limits of this application are the incompleteness of DNA barcode databases, the identification of optimal primers set, and the gap in the species sequences. The influence of the incompleteness of DNA barcode libraries on species diversity indices, ecological indicators, and ecological status assessment in transitional waters of the southeast Mediterranean were analysed, underlying the importance to implement DNA barcode libraries and to put an effort toward specific species at a local level.The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. The morphological identification of benthic macroinvertebrates is the current tool for their assessment. Recently, DNA-based tools have been proposed as effective alternatives. The main current limits of DNA-based applications include the incompleteness of species recorded in the DNA barcode reference libraries and the primers bias. Here, we analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species. The ecological quality status assigned through the potential application of both approaches to the analysed transitional water ecosystems was different in 27% of sites. We also analysed the inter-specific genetic distances to evaluate the potential application of the DNA metabarcoding method. Overall, this work highlights the importance to expand the barcode databases and to analyse, at the regional level, the gaps in the DNA barcodes.
Highlights
A key global challenge in the 21st century is to maintain the supply of clean water and other aquatic ecosystem services without affecting the supporting biodiversity and ecosystem processes that underpin their sustainability
The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments
We analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species
Summary
A key global challenge in the 21st century is to maintain the supply of clean water and other aquatic ecosystem services without affecting the supporting biodiversity and ecosystem processes that underpin their sustainability. Extensive national and international regulations have been adopted to protect aquatic ecosystems and water resources, including the Water Framework Directive (EC, 2000, Directive 2000/60/EC-WFD), the Marine Strategy Framework Directive (EC, 2008, Directive 2008/56/EC-MSFD), the Swiss Water Protection Ordinance (WPO, Swiss Federal Council 1998), the Clean Water Act (CWA, 1972) of the US Environmental Protection Agency, and the United Nations Convention on the Law of the Sea (UNCLOS, 1982). The WFD indicates specific biological quality elements (BQEs), such as fish, benthic macroinvertebrates, and phytoplanktonic benthos to assess the ecological quality status (EQS) To evaluate these elements, the directive requires the development and validation of tools mainly based on taxonomic identification and composition, abundance, and species sensitivity [2,3,4,5,6,7,8]. They include descriptors based on the individual body size [9,10,11,12], functional rates, such as the decomposition of dead organic matter [13,14,15,16,17,18,19,20,21], and ecosystem thermodynamics [22]
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