New DNA-based technologies for assessing the biodiversity of aquatic invertebrates – aquaDNA

In 2000, the European Union published the Water Framework Directive (WFD), with the goal of achieving "good status" for all surface waters by 2015, putting for the first time the ecological quality in the very heart of the environmental policies of European member states (European Council, 2000). In France, the normalized IBGN (Indice Biologique Global Normalisé) has been used at the national scale for about 20 years (norm NF T 90-350 in AFNOR, 1992, 2004) but this method is no longer satisfying due to severe inconsistencies with WFD, e.g. the IBGN index is not type specific: the same scoring system and quality class boundaries are used for all types of rivers without considering “reference conditions”. Moreover the IBGN sub-metrics did not take into account taxon abundances. To overcome the technical shortcomings of the French biotic index in the WFD implementation framework, the development of a new biotic index, i.e. the MultiMetric Invertebrate Index (I2M2), was designed for the invertebrate-based ecological assessment of French wadeable streams (Mondy et al. 2012).
At the technical level, since 2005, the output of DNA sequencers has increased dramatically, with 50,000 to 100,000 times more sequence data produced by a sequencing run. We can even expect further improvements in the near future. In this technical context, it is tempting to apply the DNA metabarcoding concept for a high throughput taxa identification of aquatic invertebrates. Such a strategy has the potential of allowing a much reliable, faster, and cheaper implementation of the WFD at the National level.
Our overall objective is to develop and validate an innovative DNA-based protocol for assessing the water quality in the context of the I2M2, taking full advantage of next generation sequencing. More specifically, we will (i) design reliable and efficient DNA metabarcodes for the relevant taxonomic groups concerned by the I2M2, (ii) build extensive reference databases for these new DNA metabarcodes, (iii) sequence the standard COI barcode for all specimens of the reference database, in order to make the link between these new metabarcodes and the standard COI barcode, (iv) develop, adjust, and validate a DNA-based protocol for estimating the I2M2, and (v) make the whole protocol available to the scientific community, as well as all the associated reference databases.
The aquaDNA consortium has been built according to these objectives, with a first partner specialized in developing innovative DNA-based methodologies in ecology and conservation, a second partner who has developed the I2M2, and finally with a small company expert in analyzing environmental DNA.