Mind the gap-analysis! – How complete are DNA barcode reference libraries for monitoring-relevant aquatic species in Europe?

Molecular species identification with DNA metabarcoding can potentially accelerate, streamline and standardise biomonitoring routines. Currently, it is tested how this new technique can be implemented for the European Water Framework Directive (WFD) and the European Marine Strategy Framework Directive (MSFD). To connect the results from DNA metabarcoding with the current monitoring routines, an extensive, high-quality DNA barcode reference database is required. Hence, a gap-analysis of the Barcode of Life Data Systems (BOLD) was performed as part of the EU-COST Action DNAqua-Net (Weigand et al. 2019), which was updated in 2021. It aimed to analyse the completeness of BOLD for species on the national WFD monitoring lists and for marine species on the ERMS (European Register of Marine Species) and AMBI (AZTI Marine Biotic Index) lists. The data were supplemented by MitoFish for freshwater fish and Diat.barcode for diatoms. Several thousands of species were included in the gap-analysis, although not all countries currently apply species-level data for all WFD biological quality elements. The barcode coverage of the different taxonomic groups varied strongly, with high levels (> 80%) for fish and freshwater vascular plants, and low levels for diatoms and freshwater plathelminths (< 15%). As a general pattern, species monitored by several countries had a higher coverage compared to those monitored only by a single country. The gap-analysis focused additionally on the availability of metadata (e.g., geographical origin of the specimen or determiner name) for the barcodes. Hence, we analysed if the data were stored public (with access to metadata) or private (without access to metadata) in BOLD or if the data were mined from GenBank (metadata are potentially available but not easy to access). Although public data were stored for many species (43% of freshwater macroinvertebrates and 21% of AMBI marine species), the proportion of species without public metadata was not neglectable (22% of freshwater macroinvertebrates and 22% of AMBI marine species). Another issue that emerged from the gap-analysis was that several deposited barcodes were identified by reverse taxonomy (RT), i.e., specimens were molecularly identified via its DNA barcode and the barcode itself is stored in BOLD with the associated species name. This can be problematic as originally misidentified samples can lead to false RT-identifications, making the data appear more trustworthy than it actually is. For the analysed freshwater macroinvertebrates, 39% of all barcodes and 65% of all public data originated from RT, impacting 11% of all monitored species. As the information about RT is only available for publicly stored data, the real impact of RT might even be higher.

Evaluation of Proximate and Heavy Metals in Twelve Edible Freshwater Macroinvertebrates of Poba Reserve Forest Assam, India.

The present study focuses on proximate and mineral compositions on 12 freshwater edible macroinvertebrate species under phylum Arthropoda and Mollusca mostly preferred by the ethnic communities around the Poba reserve forest of Assam, India. The analysis revealed protein was the most abundant nutrient for all the species; followed by carbohydrates and fats. The highest protein content was in Lobothelphusafungosa, (50.50%), total carbohydrate in Bellamyabengalensis (22.54%) and fats in Sartorianaspinigera (16.32%). Ash, fibre and moisture were highest in Corbiculaassamensis (12.46%), Sartorianaspinigera (11.41%) and Pilaglobosa (63.72%) respectively. Among the minerals, Calcium, Copper, Iron, Manganese, and Zinc were recorded highest in Bellamyabengalensis (138.62 mg/100g) Macrobrachiumassamense (2.73 mg/100g), Sartorianaspinigera (35.02 mg/100g), Macrobrachiumassamense (11.42 mg/100g) and Lethocerusindicus (3.71 mg/100g) respectively. Heavy metals (Lead, Cadmium, Molybdenum and Mercury) were absent in all the species under study. The freshwater macroinvertebratesanalyzed could form a baseline for future non-conventional food resources of considerable nutritive value.

Nestedness and turnover of riverine species and functional diversity using eDNA and traditional approaches

Accurately assessing community diversity in time and space, and linking these patterns to ecological theory, is essential for effective environmental monitoring. Freshwater macroinvertebrates are an important group of taxa routinely used for riverine environmental assessments due to their wide biological, functional and phylogenetic diversity and their responses to environmental factors. Recently, eDNA metabarcoding based sampling and identification has been shown to increase the accuracy of biodiversity assessments, while reducing cost and time, compared to traditional methods. Here, we present results from a field comparison of eDNA versus traditional riverine biodiversity techniques to assess freshwater macroinvertebrates. In addition, we investigated the effects of landuse and seasonality on community and functional diversity, to infer the underlying regional ecological temporal and spatial dynamics. Comparison of biodiversity dynamics based on traditional and eDNA survey methods showed significant differences in taxonomic groups identified between methods, landuse type, and method x season interactions. Our findings are the first example of eDNA derived functional spatio-temporal and dynamics, indicating that the regional shifts in diversity and function are linked to regional seasonal fluctuations in fine particle matter versus localized landuse type. Beta diversity components (nestedness and turnover) differed significantly along the environmental gradient, but in different directions, for each methodology. Overall, our findings show that eDNA based ecological assessment is effective in assessing temporal and spatial diversity and functional dynamics of macroinvertebrates, while demonstrating that these data can be used to infer effective biodiversity assessment and management strategies.

Nestedness and turnover of riverine species and functional diverity using eDNA and traditional approaches.

Accurately assessing community diversity in time and space, and linking these patterns to ecological theory, is essential for effective environmental monitoring. Freshwater macroinvertebrates are an important group of taxa routinely used for riverine environmental assessments due to their wide biological, functional and phylogenetic diversity and their responses to environmental factors. Recently, eDNA metabarcoding based sampling and identification has been shown to increase the accuracy of biodiversity assessments, while reducing cost and time, compared to traditional methods. Here, we present results from a field comparison of eDNA versus traditional riverine biodiversity techniques to assess freshwater macroinvertebrates. In addition, we investigated the effects of landuse and seasonality on community and functional diversity, to infer the underlying regional ecological temporal and spatial dynamics. Comparison of biodiversity dynamics based on traditional and eDNA survey methods showed significant differences in taxonomic groups identified between methods, landuse type, and method x season interactions. Our findings are the first example of eDNA derived functional spatio-temporal and dynamics, indicating that the regional shifts in diversity and function are linked to regional seasonal fluctuations in fine particle matter versus localized landuse type. Beta diversity components (nestedness and turnover) differed significantly along the environmental gradient, but in different directions, for each methodology. Overall, our findings show that eDNA based ecological assessment is effective in assessing temporal and spatial diversity and functional dynamics of macroinvertebrates, while demonstrating that these data can be used to infer effective biodiversity assessment and management strategies.