Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species

Abstract

Diatoms are valuable bioindicators and their traditional classification and identification are mainly based on the morphological characteristics of their frustules. However, in recent years, DNA-based methods have been proposed and are rapidly growing in the scientific literature as a complementary tool to assess the ecological status of freshwaters. Diatom-based ecological status assessment uses indices calculated from sensitivity and tolerance values as well as relative abundance of species. Correct assessment requires an accurate identification of species. In the present study, diatom assemblages of an oxbow lake were investigated using light and scanning electron microscopy as well as metabarcoding using rbcL marker, and the identification results were compared, intending to match barcode sequences of species that are currently missing in the diatom reference database. The investigated oxbow is an important wetland for bird conservation, although it is impacted by land use. Taxon lists based on morphology and metabarcoding considerably differed when bioinformatics analysis involved DADA2 pipeline with Diat.barcode database. Previously unknown sequence variants of four pennate species were found with additional BLAST search. Using phylogeny and p-distance calculations sequences could be matched to three small-celled naviculoid species that were found under a microscope. One of them was found to be a new species of the genus Mayamaea and was described as a new species, Mayamaea ectorii. Additionally, spatial distribution maps for several small-celled naviculoid species are provided for the Hungarian territory.

eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea

“…In comparison, Syndiniales is only represented by 72 species and accounts for 8,977 reference sequences. One approach to improve taxonomic resolution is to combine molecular approaches with morphological analysis [ 63 , 64 ]. Accordingly, we found conventional morphological analysis complemented eDNA metabarcoding by increasing the number of dinoflagellate taxa identified.…”

Comparison of Illumina MiSeq and microscopy methodologies for the analysis of diatom communities in five estuaries along the southern coast of the Korean Peninsula

“…However, although detailed identi cation of each diatom cell is important, sample size must also be considered to obtain reliable results when analyzing diatom communities [10,38]. One of the reasons why microscopy is limited in the analysis of communities (even though species-level identi cation is possible) is that substantial human resources and time are required to process samples [8,12].…”

“…Microscopy studies, which are based on morphology, have led to the development of phylogenetic systematics for the taxonomic classi cation of diatoms [9]. However, community analysis based on morphology has many limitations [10,11]. Although the morphological characteristics of each diatom species are relatively clear, extensive knowledge and expertise are still required for identi cation [10].…”

“…However, community analysis based on morphology has many limitations [10,11]. Although the morphological characteristics of each diatom species are relatively clear, extensive knowledge and expertise are still required for identi cation [10]. In addition, microscopic analysis requires considerable effort, and there is a limit to the number of samples that one researcher can handle [12].…”

“…In addition, microscopic analysis requires considerable effort, and there is a limit to the number of samples that one researcher can handle [12]. Therefore, a method that can compensate for the limitations of microscopic analysis is needed [10,12].…”