Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Abstract

Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time-consuming and needs in-depth knowledge of the organisms under investigation, as nonhomoplastic species-specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence-based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA-based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy.

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

“…Research on micro-eukaryotes was relatively common, with multiple studies being conducted on the foraminifera, as well as diatoms and a number of other protist taxa (e.g. Bradford et al 2013;Lejzerowicz et al 2014;Zimmermann et al 2015). Various invertebrate taxa were investigated in 18 studies (e.g.…”

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

“…The accuracy of metabarcoding-based taxonomic inferences relies on the retrieval of a wide range of taxonomic groups from a given environmental sample using the appropriate barcode, primers, and amplification conditions (Deagle et al, 2014;Kress et al, 2015), and on the completeness of the reference database (Zepeda Mendoza et al, 2015). Some attempts have been performed to compare morphological vs. metabarcodingbased taxonomic inferences; yet, results are inconclusive as some studies do not apply both approaches to the same sample and/or have focused on a particular taxonomic group Carew et al, 2013;Zhou et al, 2013;Gibson et al, 2014;Cowart et al, 2015;Zimmermann et al, 2015). A recent study (Gibson et al, 2015) has performed morphological and metabarcoding-based taxonomic identification on the same freshwater aquatic invertebrate samples, but limited their visual identifications to family level.…”

Multigene Assessment of Biodiversity of Diatom(Bacillariophyceae) Assemblages from the Littoral Zone of the Bohai and Yellow Seas in Yantai Region of Northeast China with some Remarks on Ubiquitous Taxa

“…The use of markers such as cox1 ( Evans et al, 2007) , rbcL ( Hamsher et al, 2011) and rDNA ( e. g. Moniz and Kaczmarska, 2009;Ruggiero et al, 2015;Zimmermann et al, 2014) has been proposed for barcoding purposes. Tests of these methods have yielded good results in differentiating closely-related species.…”