Green algae (Viridiplantae) in sediments from three lakes on Vega Island, Antarctica, assessed using DNA metabarcoding

Investigating the effects of anthropogenic stressors on lake biota using sedimentary DNA

“…Chlorophytes, also known as green algae, do not leave many morphological diagnostic features in the sediments (with a few exceptions such as Pediastrum cell nets), and thus long-term reconstruction of this phytoplanktonic group largely depends on the availability of monitoring data, which are limited. To our knowledge, sedDNA studies specifically targeting chlorophytes are still rare (Fonseca et al, 2022). However, the reconstruction of the long-term dynamic of microbial eukaryotic communities was successful at recovering archived DNA of chlorophytes (Capo et al, 2016(Capo et al, , 2017Gauthier et al, 2022;Ibrahim et al, 2021), providing insight into the response of this specific group of algae to environmental change.…”

Genetic Markers for Metabarcoding of Freshwater Microalgae: Review

“…The ITS2 region has been chosen for studying green algae s.l. (Viridiplantae) in a series of studies of the Antarctic region [72][73][74]105]. The plastid region rbcL is widely used for diatom metabarcoding, and also, primers for identifying Eustigmatophyceae have been designed and tested [97].…”

“…The PR2 (Protist Ribosomal Reference) database-a catalog of unicellular eukaryote small subunit rRNA sequences with curated taxonomy-is used less often. In a series of studies on Antarctic green algae [72][73][74], the sequences were annotated using a recently established reference dataset PLANiTS, which included the sequences of Viridiplantae ITS1, ITS2 and entire ITS sequences, including both Chlorophyta and Streptophyta [107]. To classify the 16S reads of freshwater diatom biofilm [103], PhytoREF, a reference database of the plastid 16S rRNA gene of photosynthetic eukaryotes, was used [108].…”

“…This marker resolves major green algae lineages (some with high bootstrap support), has a high resolution for taxonomic assessment (enables the most species to be distinguished) and a high level of universality (i.e., in primers for PCR) [127] (and references in it). This region was successfully used in the first studies of the diversity of Viridiplantae (including green microalgae) in the Antarctic using the metabarcoding approach in soil and rock surfaces samples [72,128], sediments from lakes [74] and glacial ice [73]. The interpretation of sequences was carried out using the PLANiTS2 database [107], and most of the taxa were identified to the species level.…”