Articles | Volume 14, issue 11
Biogeosciences, 14, 2741–2754, 2017
Biogeosciences, 14, 2741–2754, 2017

Research article 06 Jun 2017

Research article | 06 Jun 2017

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

Raphaël Morard1, Franck Lejzerowicz2, Kate F. Darling3,4, Béatrice Lecroq-Bennet5, Mikkel Winther Pedersen6, Ludovic Orlando6, Jan Pawlowski2, Stefan Mulitza1, Colomban de Vargas7,8, and Michal Kucera1 Raphaël Morard et al.
  • 1MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
  • 2Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
  • 3School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FE, UK
  • 4School of Geography and GeoSciences, University of St Andrews, Fife, KY16 9AL, UK
  • 5Okinawa Institute of Sciences and Technology Graduate University, 1919-1 Tancha, Onna-son 904-0495, Japan
  • 6Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350K, Denmark
  • 7Centre National de la Recherche Scientifique, UMR7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France
  • 8Sorbonne Universités, UPMC Univ Paris 06, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France

Abstract. Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including non-fossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.

Short summary
The exploitation of deep-sea sedimentary archive relies on the recovery of mineralized skeletons of pelagic organisms. Planktonic groups leaving preserved remains represent only a fraction of the total marine diversity. Environmental DNA left by non-fossil organisms is a promising source of information for paleo-reconstructions. Here we show how planktonic-derived environmental DNA preserves ecological structure of planktonic communities. We use planktonic foraminifera as a case study.
Final-revised paper