Abstract
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.
Highlights
With over two-thirds of the planet covered by oceans, deepsea deposits form the most extensive archive of the Earth’s recent history
Because we required reads to be present in a minimum of two samples or to show a minimal abundance of 10 in the entire dataset, the retained dataset was reduced to 697 unique sequences of planktonic foraminifera (e-ribotypes), which represent a total of 486 435 reads (∼ 0.63 % of the total dataset, Supplement 1)
Assuming that environmental DNA (eDNA) deposited on the seafloor is preserved through time, marine sediments should contain a remarkable ancient DNA archive of the history of the complete plankton communities
Summary
With over two-thirds of the planet covered by oceans, deepsea deposits form the most extensive archive of the Earth’s recent history. Deep-sea sediments are rich in DNA, with 0.31 ± 0.18 g of DNA per square meter in the surface layer, and more than 90 % of this DNA is extracellular (Dell’Anno and Danovaro, 2005) This means that DNA from many organisms is preserved after their death in the sediment and the high abundance of the DNA indicate that at least a part of the DNA pool derives from organisms living in the water column above the sediment (Lejzerowicz et al, 2013). This potential has been demonstrated in a range of other depositional environments, such as cave sediments, lake and ice cores, where the dynamics of plant and animal communities could be followed over 50 kyr (Pedersen et al, 2015)
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