No abstract

Freshwaters worldwide face serious threats, making their protection increasingly important. Freshwater monitoring has historically produced valuable data and continues to develop. Rapid improvements to biomolecular techniques are revolutionizing the way scientists describe biological communities and are bringing about major changes in biomonitoring. Combined with high‐throughput sequencing, DNA metabarcoding is fast and cost‐effective, generating massive amounts of data. In a world with numerous ecological threats, “big data” constitute a tremendous opportunity to improve the efficiency of biological monitoring. These fundamental changes in biomonitoring will require freshwater ecologists and environmental managers to reconsider how they handle large amounts of data.

In recent years, remarkable progress has been made in developing environmental DNA metabarcoding. However, its ability to quantify species relative abundance remains uncertain, limiting its application for biomonitoring. In diatoms, although the rbcL gene appears to be a suitable barcode for diatoms, providing relevant qualitative data to describe taxonomic composition, improvement of species quantification is still required. Here, we hypothesized that rbcL copy number is correlated with diatom cell biovolume (as previously described for the 18S gene) and that a correction factor (CF) based on cell biovolume should be applied to improve taxa quantification. We carried out a laboratory experiment using pure cultures of eight diatom species with contrasted cell biovolumes in order to (1) verify the relationship between rbcL copy numbers (estimated by qPCR) and diatom cell biovolumes and (2) define a potential CF. In order to evaluate CF efficiency, five mock communities were created by mixing different amounts of DNA from the eight species, and were sequenced using HTS and targeting the same rbcL barcode. As expected, the correction of DNA reads proportions by the CF improved the congruence between morphological and molecular inventories. Final validation of the CF was obtained on environmental samples (metabarcoding data from 80 benthic biofilms) for which the application of CF allowed differences between molecular and morphological water quality indices to be reduced by 47%. Overall, our results highlight the usefulness of applying a CF factor, which is effective in reducing over‐estimation of high biovolume species, correcting quantitative biases in diatom metabarcoding studies and improving final water quality assessment.

No abstract

bioinformatics treatments may be used for DNA freshwater monitoring. Our study is a proof of concept where taxonomy-and clustering-free approach is presented, that we believe is a step forward a standardized and comparable DNA bioassessment, complementary to morphological methods.

Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high‐throughput sequencing (HTS) and meta‐barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species‐level resolution. In this study, we analyzed the effect of the SST on the resulting diatom‐based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom‐specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%–99%). An OTU‐based quality index (IdxOTU) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed IdxOTU revealed significant correlations between the IdxOTU values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade‐off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring.

No abstract

Climate change is predicted to increase drought occurrence and severity in small continental watercourses. Here, we studied the structure and the functional diversity of benthic diatom assemblages in lowland intermittent and permanent watercourses of the Carpathian Basin. We assumed that the community structure of intermittent and permanent watercourses would be markedly diff erent, and the functional diversity in both would be strongly influenced by autumn drought. We found that intermittent streams were primarily characterized by small-sized generalists and aerophilic taxa, while permanent watercourses were inhabited by large-sized planktic or fast moving groups. The functional richness was significantly lower in intermittent than in permanent streams. This decrease in the functional richness of benthic algal communities may negatively aff ect the functioning of lotic algal communities. We conclude that diatom assemblages in lowland intermittent watercourses are sensitive indicators of changes in ecosystem properties, and should be considered in appropriate evaluation and management of extreme climatic events on aquatic ecosystems.