Benthic diatom metabarcoding: developing new approaches to research and biomonitoring in aquatic ecosystems

Identifier:  TDX:4057

Handle: https://hdl.handle.net/20.500.11797/TDX4057

Authors:  Pérez Burillo, Javier

Abstract:
Diatoms have been widely studied partly because of their great ecological importance and the fact that they are excellent bioindicators. However, the identification of diatoms at the species level is a time-consuming and taxonomically demanding task. Recently, DNA metabarcoding has been considered as an alternative to morphological identifications based on light microscopy (LM), although there are several factors that may decrease the effectiveness of metabarcoding. The main objective of this thesis is to evaluate the applicability of DNA metabarcoding for monitoring aquatic systems under the Water Framework Directive, as well as to address ecological and biogeographical questions. Our results indicate that metabarcoding, based on the chloroplastic marker rbcL, constitutes an effective alternative to LM for monitoring Mediterranean rivers, such as those of Catalonia, mainly because the most common benthic diatom species in these rivers are represented in the reference library. By contrast, marine species are less represented, which means that metabarcoding is not currently an alternative to LM in coastal systems, but it is a complementary tool capable of detecting species that are difficult to identify by LM, such as small, delicate species or species lacking frustules. We have also seen that the choice between the two rbcL markers currently used in metabarcoding has few implications for monitoring programmes, but does have implications for biodiversity studies. This thesis also shows how genetic variants within several diatom species complexes differ in their ecological preferences and spatial distribution. In addition, the analysis of a global database (rbcL) of freshwater diatoms has allowed us to observe that pennate diatoms show higher intraspecific diversity than centric diatoms and to identify four common phylogeographic patterns among the species analysed.