Abstract
BackgroundContinuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family.Methodology/Principal FindingsWe analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay.Conclusions/SignificanceIdentification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study.
Highlights
Diversity assessments of eukaryotic unicellular organisms, commonly referred to as protists, are often constrained by their restricted number of morphological features that can be used for species differentiation, as well as by morphological stasis and phenotypic plasticity, which affect proper taxonomic assignment
In the present Next Generation Sequencing (NGS) study we explore the biodiversity of a planktonic diatom family, the Leptocylindraceae, and the distribution of its member species
Rarefaction curves constructed with the total Leptocylindraceae dataset (Figure S1 A & B) showed V4 Operational Taxonomic Units (OTUs) reaching a plateau at a 97% similarity while V9 reached a plateau at 95%
Summary
Diversity assessments of eukaryotic unicellular organisms, commonly referred to as protists, are often constrained by their restricted number of morphological features that can be used for species differentiation, as well as by morphological stasis and phenotypic plasticity, which affect proper taxonomic assignment. Metabarcoding of PCR-amplified discriminative nucleotide markers from environmental DNA allows tracing these organisms directly in their environment without the need for cultivation. In this way spatial patterns and seasonal distribution can be reconstructed and diversity explored more extensively by using sequences as proxies. The latter approach enables discovery of new taxa associated to newfound sequences that cannot be assigned to any known organism. We use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family
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