The application of DNA sequence data for the identification of benthic nematodes from the North Sea

Abstract

Nematodes or roundworms represent one of the most diverse and dominant taxon in marine benthic habitats. Whereas a morphological identification of many species is challenging, the application of molecular markers represents a promising approach for species discrimination and identification. In this study, we used an integrative taxonomic approach, combining both molecular and morphological methods, to characterize nematodes of distinct sex and ontogenetic stages from three sampling sites of the North Sea. Morphospecies were discriminated after first visual determination, followed by a molecular analysis of the nuclear 28S rDNA: D2-D3 marker. By linking each sequence to a morphological voucher, discordant morphological identification was subjected to a so-called reverse taxonomic approach. Molecular operational taxonomic units (MOTUs) and morphospecies were compared for all of the three sampling sites to assess concordance of methodology. In total, 32 MOTUs and 26 morphospecies were assigned, of which 12 taxa were identified as described species. Both approaches showed high concordance in taxon assignment (84.4 %) except for a cluster comprising various Sabatieria species. Our study revealed the high potential of the analyzed fragment as a useful molecular marker for the identification of the North Sea nematodes and highlighted the applicability of this combined taxonomic approach in general.

Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding

“…However, this technique often demands taxa-specific optimization and several processing steps. Therefore, meiofauna barcoding surveys which often focus on identification of voucher specimens only (Vogt et al, 2014;Avó et al, 2017) may underestimate the true diversity (Tang et al, 2012) and consequently the importance of meiofauna.…”

“…Faunistic assessments are very important for understanding species relationships to the environment and DNA-based delimitation methods are widely used. Despite the fact that the accuracy of metabarcoding and MALDI-TOF MS strongly depend on reference libraries, DNA databases are remarkably poor in case of meiofauna organisms, even from well-studied areas like the North Sea (e.g., Vogt et al, 2014). Therefore, in this study, we aim at comparing the efficiency of metabarcoding and MALDI-TOF MS for community studies of previously unsampled study sites by sampling a tidal flat and using some samples for building up DNA and mass spectra libraries and others for assessing biodiversity and community structures.…”

Identification of North Sea molluscs with DNA barcoding

“…Following the guidelines of Collins & Cruickshank (2012), we aim at (i) assembling a DNA COI library from specimens identified morphologically to species level, (ii) testing the efficacy of this DNA library with simulations of sequence-based specimen identifications and (iii) exploring the possible causes of incongruence between morphological and sequence-based identifications. This study is part of the ongoing molecular characterization of the North Sea marine fauna conducted at the German Centre for Marine Biodiversity Research of the Senckenberg Institute (Laakmann et al 2013;Knebelsberger & Thiel 2014;Markert et al 2014;Vogt et al 2014).…”

Six new and one known species of Geomonhystera (Nematoda, Monhysteridae) from moss, an epiphytic plant and soil in México and Ecuador

“…New sequences were submitted to the GenBank database under the accession numbers MG077077-MG077081. The new sequences of the D2-D3 of 28S rRNA gene were aligned using ClustalX 1.83 (Thompson et al 1997) with published sequences of other Monhysteridae and outgroup taxa (Litvaitis et al 2000;Van Gaever et al 2009;Vogt et al 2014;Schenk et al 2017). Outgroup taxa were selected based on the phylogenetic tree published by Van Megen et al (2009).…”