Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

Fit for purpose? Evaluating benthic invertebrate DNA metabarcoding for ecological status class assessment in streams under the Water Framework Directive

The ecological state of aquatic ecosystems is systematically monitored using various bioindicators in many countries worldwide. In the European Union, freshwater biomonitoring is the central component of the EU Water Framework Directive (WFD, 2000/60/EC) and currently based on morpho-taxonomic methods. DNA metabarcoding is a novel approach to assess the ecological state fast and efficiently based on organismal DNA signatures and thereby support and upscale biomonitoring. However, compliance of metabarcoding with existing morpho-taxonomic methods must be ensured prior to official implementation. Thus, this study, co-designed by research institutions and environmental agencies, explored necessary key parameters and performed method intercalibration for the implementation of metabarcoding into WFD assessments of running waters. We focussed on benthic invertebrates as the most commonly used bioindicators. We analysed 170 invertebrate samples collected as part of the German federal state WFD routine stream biomonitoring, first via microscopic determination and then using metabarcoding. Our goals were to quantify overlap in i) taxonomic composition and ii) ecological status derived with both methods. For this purpose, we established data harmonisation measures to integrate invertebrate metabarcoding data into the official national WFD classification modules considering abundance and presence/absence data. Our results revealed a high (ca. 70 %) overlap of bioindicator taxa found with both methods. Metabarcoding identified significantly more small invertebrate taxa and detected similar proportions of the important bioindicator 'EPT' taxa (mayflies, stoneflies, caddisflies). Despite deviations in some detected bioindicator taxa, the derived ecological status classes were highly correlated between methods, particularly after intercalibration (R2 = 0.74, Spearman rho = 0.86). Regardless of whether we used abundance or presence/absence data, the resulting stream type classifications showed strong agreement. Thus, our study not only demonstrates the consistency of the methods for the stream types analysed but is also the first to operationalise a path to integration of metabarcoding data into the WFD assessment modules based on formal intercalibration guidelines.

The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases

The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.

Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.

Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches

Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.