Collaborative partner 9 - Prof. Jan Pawlowski and team, University of Geneva, Switzerland
P9 focused on Foraminifera – a group of abundant and highly diversified marine protists that mineralize carbonate shells (tests) widely used as proxies for past and present environmental conditions. Foraminifera are particularly suitable for eDNA studies because the exceptional variability of their ribosomal genes as compared to other eukaryotes facilitate their specific amplification and identification at the species level in next-generation sequencing (NGS) datasets. Over the course of BioMarKs, P9 achieved the following tasks:
- Development of foraminiferal specific DNA barcodes and setup of the Foram Barcoding Database (FBD) http://forambarcoding.unige.ch/
- Comparison of microscopic and eDNA inventories of foraminiferal diversity
- Discovery and inventory of benthic foraminiferal diversity in water column samples
- Use of foraminiferal DNA barcodes for applied NGS-based biomonitoring
BioMarKs allowed completing the database of foraminiferal DNA barcodes from EU species. The FBDatabase contains currently >3000 sequences of 18S rDNA hypervariable regions, many of them obtained from specimens collected during the BioMarKs sampling. The completeness and accuracy of FBD was essential for correct taxonomic assignment of environmental NGS generated dataset, especially those aimed at environmental monitoring.
The analysis of BioMarKs foraminiferal data permitted to highlight specific biases related to eDNA studies. rDNA Intragenomic polymorphism can reach up to 5% sequence divergence in certain foraminiferal species. Comparison between foraminiferal NGS and microscopic counts datasets from the same BioMarKs samples shows that all common identified morphospecies are present in NGS data, the later being dominated by inconspicuous taxa whose morphological identity remained enigmatic. The most spectacular finding was the pervasive and significant presence of DNA sequences of benthic species in planktonic samples, including diverse foraminiferal taxa from the order Rotaliida (in orange in Fig. 9). Surprisingly, only few OTUs present in water samples were also found in sediment samples, which were dominated by monothalamids and environmental clades. The origin of these benthic species in the plankton remained enigmatic. They may correspond to (i) propagules dispersed by the water currents, (ii) unknown pico-sized species, or (iii) extracellular DNA of benthic species preserved in the water.
Figure 9. Order-level taxonomic diversity of foraminiferal eDNA sequences present across size-fractions and habitats in BioMarKs samples (GLO – Globigerinida, ROT – Rotaliida, TEX – Textulariida, MIL – Miliolida, MON – Monothalamids, ENV – environmental clades, UNK – undetermined foram lineages).