BIOMARKS

Nucleic acid based studies of marine biodiversity often focus on Kingdom-level diversity or specifically target well-characterised lineages. However, these approaches miss large parts of the diversity of less studied groups, which are likely to harbour a wealth of unknown lineages and play significant ecological roles. Among these elusive groups are the "Endomyxa" (Rhizaria), a possibly polyphyletic collection of ubiquitous, but still largely understudied lineages comprising parasites (e.g. Ascetosporea, Phytomyxea), free-living amoebae (e.g. Vampyrellida, Gromia, Filoreta) and flagellates (e.g. Tremula, Aquavolon), and several environmental lineages of unknown phenotype. Using Endomyxa-biased primers targeting the hypervariable region V4 of the 18S rRNA gene, we explored the biodiversity of Endomyxa in marine samples from European coastal sites and compared it to that found in pan-eukaryote V4 libraries of the same samples. In total 458 endomyxan OTUs were identified, 38% of which only detected by the specific primer approach. They are for the most part distinct from published reference sequences, and include both novel diversity within known clades, and putative novel lineages. The data revealed variations in endomyxan assemblages related to habitat (benthic vs. pelagic, sampling site), mode of nutrition (parasitic vs. free-living) and nucleic acid type (DNA vs. RNA). Overall, the vast majority of endomyxan diversity occurs in the sediments (including Vampyrellida, Filoreta spp., and OTUs affiliated to the environmental "Novel Clade 12") where they form large and active communities and comprise many uncharacterised lineages.