The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

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.

Trobajo R., Clavero E., Chepurnov V.A., Sabbe K., Mann D.G., Ishihara S. and Cox E.J. 2009. Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae). Phycologia 48: 443–459. DOI: 10.2216/08-69.1. Nitzschia palea (Kützing) W. Smith is believed to be a widely distributed diatom and is common in various lotic and lentic freshwater habitats. However, it is also taxonomically problematic. As part of a multidisciplinary study of this diatom, 25 clones identified morphologically as N. palea were isolated from different freshwater habitats around the world (Belgium, Brazil, Egypt, India, Japan, Paraguay, Spain, Sri Lanka and the United Kingdom). Morphological and genetic diversity (using the hypervariable D1–D2 domains of LSU rDNA) were investigated, and an almost complete set of interclonal crossing experiments was carried out. Results indicate that N. palea is not a simple, homogeneous taxon and that N. palea will probably have to be split into ...

The taxonomy of several small-celled, ecologically significant Nitzschia species, which are frequently confused with each other or whose names are misapplied, is clarified. Following an examination of type material and modern samples by light and electron microscopy, it was concluded that N. frustulum (Kützing) Grunow, N. inconspicua Grunow, N. soratensis E. Morales & Vis and N. invisitata Hustedt are independent species. No morphological basis was found for separating N. frustulum var. subsalina Hustedt or N. boliviana E. Morales & Vis from N. inconspicua and they are therefore placed in synonymy with N. inconspicua. Nitzschia soratensis, described recently from Bolivia, has previously been misidentified in Europe, either as N. inconspicua (from which it differs most obviously in having more bluntly rounded poles, striae within the raphe canal that are composed of triplets, and fibulae that can be seen in light microscopy to widen at their bases) or as N. abbreviata Hustedt ex Simonsen (from which it differs in pore ultrastructure). Nitzschia frustulum resembles N. inconspicua in every morphological feature examined, but with wider valves and consistently higher maximum length.