Using sedaDNA to reconstruct planktonic communities across 385’000 years old marine sedimentary core from a tropical sea

International audienc

In the last ten years, sedimentary ancient DNA (sedaDNA) becomes a new proxy for paleoceanographic analyses that provide information about large range of non-fossilized taxa. Usually, the sediment samples destinated for sedaDNA study are immediately frozen after collection or stored in special buffer to preserve the DNA. However, there are many cores that have been collected long time before the advent of paleogenomics and that are commonly refrigerated and stored at 4°C. Here, we test whether such cores can be used as a source of ancient DNA, by analysing the sedaDNA samples from 36 meters long marine gravity core that was stored during 14 years at 4 °C. The core MD05-2920 was retrieved during the MD148/PECTEN – Images XII cruise, in Bismarck Sea, off New Papua Guinea, and records the past 385 ka. We analysed samples from 20 layers spanning the interval from 1.6 ka to 384 ka, where isotopic measures of ∂18O showed significant paleoceanographic changes. We started by analysing a universal eukaryotic marker, the V9 (170 bp) region of the 18S rRNA. However, the obtained datasets were dominated by sequences belonging to species of fungi and amoebae that probably originated from post-collection storage. More data were obtained by using markers specific to selected marine taxa, such as foraminifera, radiolaria, and diatoms. The analysis of these data show clearly that the DNA is preserved in marine sediment down to 385 ka old layers. Our study also shows a possibility to exploit the sedaDNA from refrigerated material stored in cores repositories.

International audienc

In the last ten years, sedimentary ancient DNA (sedaDNA) becomes a new proxy for paleoceanographic analyses that provide information about large range of non-fossilized taxa. Usually, the sediment samples destinated for sedaDNA study are immediately frozen after collection or stored in special buffer to preserve the DNA. However, there are many cores that have been collected long time before the advent of paleogenomics and that are commonly refrigerated and stored at 4°C. Here, we test whether such cores can be used as a source of ancient DNA, by analysing the sedaDNA samples from 36 meters long marine gravity core that was stored during 14 years at 4 °C. The core MD05-2920 was retrieved during the MD148/PECTEN – Images XII cruise, in Bismarck Sea, off New Papua Guinea, and records the past 385 ka. We analysed samples from 20 layers spanning the interval from 1.6 ka to 384 ka, where isotopic measures of ∂18O showed significant paleoceanographic changes. We started by analysing a universal eukaryotic marker, the V9 (170 bp) region of the 18S rRNA. However, the obtained datasets were dominated by sequences belonging to species of fungi and amoebae that probably originated from post-collection storage. More data were obtained by using markers specific to selected marine taxa, such as foraminifera, radiolaria, and diatoms. The analysis of these data show clearly that the DNA is preserved in marine sediment down to 385 ka old layers. Our study also shows a possibility to exploit the sedaDNA from refrigerated material stored in cores repositories.

International audienc

In the last ten years, sedimentary ancient DNA (sedaDNA) becomes a new proxy for paleoceanographic analyses that provide information about large range of non-fossilized taxa. Usually, the sediment samples destinated for sedaDNA study are immediately frozen after collection or stored in special buffer to preserve the DNA. However, there are many cores that have been collected long time before the advent of paleogenomics and that are commonly refrigerated and stored at 4°C. Here, we test whether such cores can be used as a source of ancient DNA, by analysing the sedaDNA samples from 36 meters long marine gravity core that was stored during 14 years at 4 °C. The core MD05-2920 was retrieved during the MD148/PECTEN – Images XII cruise, in Bismarck Sea, off New Papua Guinea, and records the past 385 ka. We analysed samples from 20 layers spanning the interval from 1.6 ka to 384 ka, where isotopic measures of ∂18O showed significant paleoceanographic changes. We started by analysing a universal eukaryotic marker, the V9 (170 bp) region of the 18S rRNA. However, the obtained datasets were dominated by sequences belonging to species of fungi and amoebae that probably originated from post-collection storage. More data were obtained by using markers specific to selected marine taxa, such as foraminifera, radiolaria, and diatoms. The analysis of these data show clearly that the DNA is preserved in marine sediment down to 385 ka old layers. Our study also shows a possibility to exploit the sedaDNA from refrigerated material stored in cores repositories.

International audienc

Using sedaDNA to reconstruct planktonic communities across 385’000 years old marine sedimentary core from a tropical sea

International audienc

Using sedaDNA to reconstruct planktonic communities across 385’000 years old marine sedimentary core from a tropical sea

International audienc

New xenophyophores (Foraminifera, Monothalamea) from the eastern Clarion-Clipperton Zone (equatorial Pacific)

Xenophyophores are large, agglutinated foraminifera that dominate the benthic megafauna in some parts of the deep sea. Here, we describe an assemblage of largely fragmentary specimens from the Clarion-Clipperton Zone (CCZ), an area of the eastern abyssal Pacific hosting large, commercially significant deposits of polymetallic nodules. We recognised 18 morphospecies of which eight yielded DNA sequences. These include two new genera and three new species, Claraclippia seminuda gen. & sp. nov., Stereodiktyoma mollis gen. & sp. nov., and Aschemonella tani sp. nov., three that are assigned to known species, Abyssalia foliformis, Aschemonella monilis and Shinkaiya contorta, and two assigned to open nomenclature forms Abyssalia aff. foliformis and Stannophyllum aff. granularium. An additional ten forms are represented only by morphology. The following seven are placed in known genera, species and open-nomenclature forms: Aschemonella? sp., Homogammina sp., Psammina multiloculata, P. aff. multiloculata, P. aff. limbata form 1 sensu Gooday et al., 2018, P. aff. limbata form 2 sensu Gooday et al., 2018, and Stannophyllum spp. The other three could not be identified to genus level. This new collection brings the total of described and undescribed species and morphotypes from the CCZ to 27 and 70, respectively, reinforcing the already high diversity of xenophyophores known from this part of the Pacific

Unmodified foraminiferal raw eDNA data in form of 'reads' with ASV, OTU and taxonomic assignations from sediment surface samples at stations REF, IF20-12, IF20-10, IF20-18, IF20-01 and IF20-04

The eDNA analysis was done using a DNeasy® PowerLyzer PowerSoil Kit (QIAGEN), processed using the DADA2 pipeline and the taxonomic assignations were estimated using a sequence bank at ID-Gene ecodiagnostics lab in Geneva Switzerland