Giant deep-sea Foraminifera are enriched in Archaea and associated lipid biomarkers in their agglutinated tests

Summary As agglutinated Foraminifera, Xenophyophores inhabit the deep ocean floor and build their tests from particles of the environment. Despite their diversity and abundance, especially in areas of commercial interest for polymetallic nodules, the role of Xenophyophores in the deep-sea ecosystem and their physiology is still poorly understood. Previous studies hypothesized that their tests provide a habitat for deep-sea microbes. To further investigate Xenophyophores and associated microbes, we analyzed diverse Xenophyophores from the Quepos plateau and seamounts off Costa Rica for their lipid biomarkers and microbial 16S rRNA gene diversity. In our data we identified archaeal glycerol dialkyl glycerol tetraethers with a high content of intact polar lipids and substantial amounts of the thaumarchaeal biomarker Crenarchaeol. This data is suggestive of a thaumarchaeal assemblage, which was independently confirmed through Illumina 16S rRNA amplicon sequencing. The spatial distribution of biomarkers we observed with mass spectrometry imaging in a section through a Xenophyophore test shows a heterogeneity, which we interpret as differences in activity, community composition and/ or growth stages of the archaeal community members. Our lipid biomarker and molecular data suggests that Thaumarchaea are associated with diverse Xenophyophores and that their tests can provide a newly discovered micro-niche for these microbes.