High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

Alexandra Schoenle,Manon Hohlfeld,Karoline Hermanns,Colomban De Vargas,Frank Nitsche,Hartmut Arndt,Frédéric Mahé

doi:10.1038/s42003-021-02012-5

Abstract

Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.

Highlights

Heterotrophic protists form a major link from bacteria and algae to higher trophic levels in the sunlit ocean
Strict bioinformatic quality control led to a final eukaryotic dataset of ~47,000 operational taxonomic units (OTUs) (~70 million reads), of which the majority (87%) could be taxonomically assigned to groups of heterotrophic protists (Supplementary Tables 1 and 2)
Keeping in mind that the number of sampled stations was more than twice as high, the eukaryotic richness in the euphotic zone of marine waters was more than twice as high (~110,000 OTUs, the majority belonged to heterotrophic protistan groups11) when compared to our deep-sea eukaryotic OTUs

Summary

Results and discussion

We could recover 31 strains of these 102 cultivated marine protists (i.e. 21 deep-sea strains, 8 surface water strains) belonging to 20 species (19 OTUs, ~170,000 reads) with a V9 sequence similarity of 100% including Stramenopiles (bicosoecids, placidids), Discoba (kinetoplastids), Alveolata (ciliates), Obazoa (choanoflagellates), Rhizaria (cercozoans), and Cryptista (cryptophyceans). This highlights the importance of cultivation-based approaches for detailed molecular and morphological description of marine protists and the proper assignment of reads produced by NGS methods. The majority of taxa recorded from the different deep-sea regions belonged either to bacterivorous groups

Predatory macro- and megafauna

Methods

Code availability