Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems

Abstract

Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystemsConservation and sustainable management of aquatic ecosystems is a priority in environmental programs worldwide. However, these aims are highly dependent on the efficiency, accuracy and cost of existent methods for the detection of keystone species and monitoring of biological communities. Rapid advances in eDNA, barcoding and metabarcoding promoted by high-throughput sequencing technologies are generating millions of sequences in a fast way, with a promising cost reduction, and overcoming some difficulties of the traditional taxonomic approaches. This paper provides an updated broad perspective of the current developments in this dynamic field presented in the special session (SS) "The use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems" of the XIX Congress of the Iberian Association of Limnology (AIL2018), held in Coimbra, Portugal. Developments presented are mainly focused on the Iberian Peninsula (Portugal and Spain, including Atlantic Macaronesian islands) but include studies in France, Germany, Finland, Russia (Siberia) and South America. The networks within which these researchers are involved are yet even broader, profiting from existing molecular facilities, and traditional taxonomic expertise, which can be viewed as a characteristic of this new research area. It was evident in the SS that the use of molecular tools is widespread, being used to study a diversity of aquatic systems, from rivers' headwaters to estuaries and coastal lagoons, and volcanic, mountain and frozen lakes to hot springs. The organisms targeted are likewise varied and include fish, macroinvertebrates, meiofauna, microalgae such as diatoms and dinoflagellates, other protists, fungi, and bacteria (cyanobacteria and other). Some studies address the whole biodiversity (i.e., all species present independently of the taxonomic group) from environmental samples of water, biofilms and preservative solution from field samples (e.g., ethanol from macroinvertebrate samples). Great advances were acknowledged in the special session, namely in the use of metabarcoding for detecting hidden biodiversity, juvenile stages, low-abundance species, non-indigenous species and toxicity potential, and ultimately for ecological monitoring of diatoms and invertebrates. Yet, several drawbacks were highlighted and need further work, which include: taxonomic gaps in the reference databases (including gaps at species level and on intraspecific variability) or absence of public databases (e.g. for meiofauna), still high sequencing costs, the need of a substantial bioinformatics effort, difficulties in establishing the amount of environmental sample necessary for a good DNA extraction and the need for testing different genetic markers to obtain accurate results.

Eco‐assessment of Değirmendere and Bulaklı streams using diatom indices from different ecoregions

“…Spatial and temporal variation in environmental variables affected the distribution of diatom assemblages in the current study, which is in agreement with findings of ecological studies (Feio et al, 2020; Freitas et al, 2021). Results of ANOSIM indicated that there was no significant difference in the diatom composition of Değirmendere and Bulaklı streams among sampling seasons.…”

“…Spatial and temporal variation in environmental variables affected the distribution of diatom assemblages in the current study, which is in agreement with findings of ecological studies (Feio et al, 2020;Freitas et al, 2021).…”

Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers

“…Consequently, efforts have been undertaken to integrate metabarcoding in freshwater monitoring (Elbrecht & Steinke, 2019;Feio et al, 2020;Leese et al, 2016;Pawlowski et al, 2018), which for organisms such as diatoms have succeeded in producing methods that are virtually ready for practical application (Apothéloz-Perret-Gentil et al, 2017;Cordier, Lanzén, Apothéloz-Perret-Gentil, Stoeck, & Pawlowski, 2019;Mortágua et al, 2019;Visco et al, 2015), whereas for others, a great deal of optimization and standardization is still needed (Pawlowski et al, 2018).…”

“…During the past decade, it was demonstrated that these constraints can at least partly be offset by molecular techniques such as DNA metabarcoding, which allows the identification of multiple taxa from environmental samples using standard genetic markers (Baird & Hajibabaei, 2012; Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, 2012). Consequently, efforts have been undertaken to integrate metabarcoding in freshwater monitoring (Elbrecht & Steinke, 2019; Feio et al., 2020; Leese et al., 2016; Pawlowski et al., 2018), which for organisms such as diatoms have succeeded in producing methods that are virtually ready for practical application (Apothéloz‐Perret‐Gentil et al., 2017; Cordier, Lanzén, Apothéloz‐Perret‐Gentil, Stoeck, & Pawlowski, 2019; Mortágua et al, 2019; Visco et al., 2015), whereas for others, a great deal of optimization and standardization is still needed (Pawlowski et al., 2018).…”

Morphological description and DNA-based association of the last instar larva of Erotesis schachti Malicky 1982 (Trichoptera: Leptoceridae), an endemic of the Iberian Peninsula

“…Therefore, new and accurate DNA-based biomonitoring methodologies are currently being developed using species-level DNA barcodes (e.g., Elbrecht et al 2017;Blackman et al 2019;Martins et al 2019). Even phylogenetic (Zhou et al 2016;Thomas et al 2020) and biodiversity conservation studies (e.g., Ruppert et al 2019;Feio et al 2020) can benefit from these DNA sequencing techniques.…”