Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

Abstract

Deep-sea floors represent one of the largest and most complex ecosystems on Earth but remain essentially unexplored. The vastness and remoteness of this ecosystem make deep-sea sampling difficult, hampering traditional taxonomic observations and diversity assessment. This problem is particularly true in the case of the deep-sea meiofauna, which largely comprises small-sized, fragile, and difficult-to-identify metazoans and protists. Here, we introduce an ultra-deep sequencing-based metagenetic approach to examine the richness of benthic foraminifera, a principal component of deep-sea meiofauna. We used Illumina sequencing technology to assess foraminiferal richness in 31 unsieved deep-sea sediment samples from five distinct oceanic regions. We sequenced an extremely short fragment (36 bases) of the small subunit ribosomal DNA hypervariable region 37f, which has been shown to accurately distinguish foraminiferal species. In total, we obtained 495,978 unique sequences that were grouped into 1,643 operational taxonomic units, of which about half (841) could be reliably assigned to foraminifera. The vast majority of the operational taxonomic units (nearly 90%) were either assigned to early (ancient) lineages of soft-walled, single-chambered (monothalamous) foraminifera or remained undetermined and yet possibly belong to unknown early lineages. Contrasting with the classical view of multichambered taxa dominating foraminiferal assemblages, our work reflects an unexpected diversity of monothalamous lineages that are as yet unknown using conventional micropaleontological observations. Although we can only speculate about their morphology, the immense richness of deep-sea phylotypes revealed by this study suggests that ultra-deep sequencing can improve understanding of deep-sea benthic diversity considered until now as unknowable based on a traditional taxonomic approach.DNA barcoding | next-generation sequencing | small subunit ribosomal RNA | microbial eukaryote | cosmopolitanism D eep-sea sediments are home for a wide range of small-sized metazoan and protistan taxa. The diversity of this meiofaunal community is difficult to estimate because its study suffers from undersampling, difficult access, and the problems involved in culturing deep-sea organisms. Additionally, most of the deep-sea species are tiny, fragile, and difficult to identify. Benthic foraminifera form one of the most abundant and diverse groups of deepsea meiofauna, found even in the deepest ocean trenches (1). Particularly in abyssal areas, a large proportion of deep-sea foraminifera belongs to early lineages characterized by simple, singlechambered (monothalamous), organic-walled or agglutinated tests, which are poorly preserved in the fossil record (2). These early monothalamous lineages traditionally classified in orders Allogromiida and Astrorhiza have been proposed to form a large radiation in the Neoproterozoic, well before the first multichambered foraminifera appeared (3). However, the assessment of their diversity is hampered by the fragment...

Molecular investigation of protistan diversity along an elevation transect of alpine lakes

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Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

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Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

“…These sequences represent eDNA exported to the seafloor from the plankton. With the recent development of the Planktonic Foraminifera Ribosomal Ref- erence Database (PFR 2 ; Morard et al, 2015), the environmental sequences belonging to planktonic foraminifera in the eDNA libraries generated by Lecroq et al (2011) can now be, for the first time, thoroughly analyzed and assigned to the morphological and cryptic species levels The extensive knowledge on the distribution and abundance of planktonic foraminiferal shells in surface sediments (Kucera et al, 2005) enabled the eDNA data to be directly compared with data derived from classical taxonomy. We thus assess to what extent the eDNA originating from plankton is representative of the source community, which is an essential prerequisite for interpretation of the eDNA archive in the sediment.…”

“…In the present study we perform new analysis on eDNA libraries generated by Lecroq et al (2011), which comprise metabarcodes from 31 abyssal sediment samples containing ∼ 78 million foraminiferal sequences derived from the 37f foraminiferal specific barcode of the 18S rDNA. The major portion (> 99 %) of the sequences could be assigned to benthic taxa and their composition was analyzed to unravel the patterns of benthic diversity on the seafloor.…”