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.

SummaryLittle is known about the potential effect of climate warming on phyllosphere fungi, despite their important impact on the dynamics and diversity of plant communities. The structure of phyllosphere fungal assemblages along elevation gradients may provide information about this potential effect, because elevation gradients correspond to temperature gradients over short geographic distances.We thus investigated variations in the composition of fungal assemblages inhabiting the phyllosphere of European beech (Fagus sylvatica) at four sites over a gradient of 1000 m of elevation in the French Pyré né es Mountains, by using tag-encoded 454 pyrosequencing.Our results show that the composition of fungal assemblages varied significantly between elevation sites, in terms of both the relative abundance and the presence-absence of species, and that the variations in assemblage composition were well correlated with variations in the average temperatures.Our results therefore suggest that climate warming might alter both the incidence and the abundance of phyllosphere fungal species, including potential pathogens. For example, Mycosphaerella punctiformis, a causal agent of leaf spots, showed decreasing abundance with elevation and might therefore shift to higher elevations in response to warming.

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