Morpho-molecular characterization of sand-dwelling dinoflagellate communities from the German Wadden Sea and insights into their spatiotemporal distribution

ABSTRACT

Benthic protist communities, including sand-dwelling dinoflagellates, are still poorly characterized worldwide and there is a lack of knowledge on their diversity and spatiotemporal dynamics. In this study, sediments were obtained from several coastal locations of the German Wadden Sea during the summer months of 2017 and 2018 to determine the diversity and spatiotemporal distribution of sand-dwelling dinoflagellates. The analyses consisted of light microscopy and the metabarcoding of small subunit (SSU) rRNA gene V4 region amplicons. Additionally, SSU rRNA sequences were newly obtained for 15 observed taxa included in a reference database and were used to taxonomically assign the obtained amplicon sequence variants (ASVs). The combination of morphological and molecular approaches allowed a deep characterization of dinoflagellate communities. Seventy-three morphospecies were detected by microscopy, while metabarcoding ASVs (amplicon sequence variants) were assigned to 116 species, resulting in a more comprehensive biodiversity inventory than achieved with either method alone. Pfiesteriaceae, Togula compacta and Thecadinium yashimaense predominated in the different sampling locations. Communities from Wilhelmshaven diverged from the others, consistent with its muddier sediment. A high level of resemblance was determined for the communities from each location, regardless of the sampling month and year, indicating a high summertime stability of benthic communities. Further efforts will be needed to characterize benthic protist diversity, as a first step in obtaining a complete picture of the habitat characteristics and physico-chemical conditions that influence benthic community composition.

Highlights

• Metabarcoding and microscopy observations provide complementary results.

• Much of the diversity of sand-dwelling dinoflagellates is uncharacterized.

• Benthic dinoflagellate communities were stable at each location in summer.

KEYWORDS:

• Benthic
• Germany
• metabarcoding
• North Sea
• protist
• sediments

Acknowledgements

MH thanks Alexander Kieneke (Senckenberg am Meer) for sharing a Maade Siel sample, and Lena Albers and Tanja Wilke (Univ. Oldenburg) for sampling on the island of Sylt. Marc Gottschling (LMU München) is thanked for kindly sharing the sequences alignment used for the phylogenetic analysis.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Supplementary information

The following supplementary material is accessible via the Supplementary Content tab on the article’s online page at https://doi.org/10.1080/09670262.2023.2279547

Supplementary table S1. Sampling details. Most samples from Wilhelmshaven were obtained from its south beach (left side of the slipway), but some of them correspond to the right side of the slipway, indicated with (R).

Supplementary table S2. List of primers used for rRNA gene sequence amplifications.

Supplementary table S3. New reference sequences obtained in this study, including the species and isolate names, location and date of isolation, the number of cells isolated and used for sequencing, the GenBank accession numbers and the length (base pairs) of the sequences.

Supplementary table S4. Summary of samples processed by metabarcoding, including the total number of reads obtained, the number of reads corresponding to dinoflagellates and the percentage they represent, and the number of dinoflagellate ASVs. Wilhelmshaven (R) corresponds to the right side of the slipway while the rest of the samples correspond to the left side.

Supplementary table S5. Table showing whether a morphospecies was only detected by light microscopy (green), by metabarcoding (yellow) or by both methods (blue) at each sampling performed. Only those morphospecies with molecular information available have been considered. The sampling dates are indicated. The final rows shaded in light grey represent the percentages of detections by each method for each sample, only taking into account those species that were observed at any sample by microscopy. The final rows shaded in dark grey represent the same percentages, but also taking into account those species detected by metabarcoding and never observed by microscopy.

WHV: Wilhelmshaven, SCH: Schillig, WGR: Wangerooge, LIST: List ferry pier, ODD: Oddewatt.

Author contributions

A. Reñé: original concept, sampling, microscopy, phylogenetics, metabarcoding, drafting and editing manuscript; N. Timoneda: metabarcoding, editing manuscript; S. Khodami: metabarcoding, editing manuscript; P. López-García: funding, editing manuscript; P. Martínez Arbizu: funding, editing manuscript; M. Hoppenrath: original concept, sampling, microscopy, funding, drafting and editing manuscript.

Notes

Additional information

Funding

AR was funded by a ‘Senckenberg Taxonomy Grant 2017’, a DAAD ‘Research Stays for University Academics and Scientists 2018’ Grant [91644317] and thanks the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). This is publication number 87 from Senckenberg am Meer Molecular and Metabarcoding Laboratory; Deutscher Akademischer Austauschdienst.