Abstract
The use of molecular tools (DNA barcoding and metabarcoding) for the identification of species and ecosystem biomonitoring is a promising innovative approach. The effectiveness of these tools is, however, highly dependent on the reliability and coverage of the DNA sequence reference libraries and it also depends on the identification of primer sets that work on the broadest range of taxa. In this study, a gap analysis of available DNA barcodes in the international libraries was conducted using the aquatic macroinvertebrate species checklist of the Apulia region in the southeast of Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more effective DNA barcode implementation effort and extensive use of the metabarcoding method. In this paper, a new combination of primers has revealed its experimental effectiveness at least on the species belonging to the three most represented taxa in the aquatic ecosystems of the Apulia region, highlighting the opportunity to develop combinations of primers useful at the regional level and the importance of studying DNA barcode gaps at the local/regional level. The DNA barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Acquatina di Frigole” in the Apulia region) and we sampled two macroinvertebrate species lacking DNA barcodes from “Aquatina di Frigole” NATURA 2000 Site IT9150003, Fabulina fabula and Tritia nitida, generated two new CO1 barcodes and added them to a DNA barcode reference library.
Highlights
It is widely recognized that biodiversity in the world is in danger, with obvious decreases each year
The success of the DNA metabarcoding method is based on the efficiency of the primer sets on the largest number of taxa [27]. In this project, using the Apulia Regional Environmental Protection Agency (ARPA, Puglia, 2011) reference checklist of benthic macroinvertebrates of the aquatic ecosystems of the Apulia region [28], we evaluated the extent of the gap in DNA barcodes in the reference libraries and identified which and how many species, belonging to 440 families, do not have their DNA barcode uploaded in the libraries
In order to investigate the degree of completeness of the barcode sequence databases for the purpose of future use in the assessment of environmental quality, we used the list of macroinvertebrate species of the ARPA, Puglia
Summary
It is widely recognized that biodiversity in the world is in danger, with obvious decreases each year. The monitoring of biodiversity, as well as the analysis of occurrence and abundance of target taxonomic groups,is essential for evaluating the health of ecosystems and environmental change in marine coastal waters, transitional waters and freshwaters [2,3,4,5]. The detection of larval stages has many advantages, like monitoring the establishment or spread of invasive populations and identification of larvae of economically important, sensitive or tolerant species, leading to an estimation of the habitat quality. The chironomids, important macroinvertebrates of freshwater communities, are often treated at the family level of Chironomidae in ecological studies or bioassessments given the difficulty in identifying specimens at lower taxonomic levels of the genus or species [11].
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