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Exploring Diversity of Marine Eukaryotes Across 385 Ka Old Gravity Core Using Sedadna

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Exploring Diversity of Marine Eukaryotes Across 385 Ka Old Gravity Core Using Sedadna Exploring diversity of marine eukaryotes across 385 ka old gravity core using sedaDNA Ines Barrenechea Angeles1,2, Luc Beaufort3, Daniel Ariztegui2 and Jan Pawlowski1,4 1 Department of Earth Sciences, University of Geneva, Geneva, Switzerland 2 Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland 3 CEREGE, Europole Mediterranéen de l'Arbois, Aix-en-Provence, France 4 Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland Contact: [email protected] EGU 2020 - BG2.2 Mon, 4 May, 16:15–18:00 Context Cores repositories store archive half cores not used for geological analysis. They are stored at 4°C, the temperature of the ocean floor from where they were recovered. Working with sedaDNA requires rigour and precautions from sampling to sequencing to avoid contaminants. In most studies, the cores are freshly recovered and MARUM core repository processed immediately. Here we test the potential of cores stored during several years. Core MD05-2920 Aim: 0.3 m ~1630 BP • Could aDNA preserved in cores stored for several years at 4°C storage? Papua Bismarck • Could obtained Papua Sea aDNA data be New Guinea usable? How: subsampling an 35 m ~384 000 BP “archive half “ core and sequencing the Recovered: 2005 specific regions of DNA extraction: 2019 Water depth: 1843m 18S rRNA gene Sedimentation rate: 10cm/ky Climate setting Interglacial Warm T° Glacial Cold T° Successional changes in species communities • Samples were selected from inter- and glacial events • Blue zone = glacial periods • Numbers in purple (y-axis) = marine isotopic stage (MIS) Tachikawa et al. (2014) Methods - Metabarcoding Sampling/ subsampling PCR DNA Sequencing Bioinformatics Amplification extraction AATTAGAGC AATTAGA TTTCAAAGG Reference GCTTTCA GCCAATTAG + AAGGGCC AGCTTTCA database AAGGGCC High throughput Illumina sequencing 15 Mio reads Precautions: • Subsampling an intact “ archive half core” Species identification • Clean working place • Negative controls Methods – regions from SSU ribosomal RNA gene To target planktonic DNA, we use several specific regions of 18S rRNA gene. V9 37f - 41f V4 diatoms (DIV4) 130 - 200 bp 320-400 bp ~ 400 bp eukaryotes foraminifera diatoms Amaral- settler et al. 2009 Pawlowski et Lecroq 2010 Zimmermann et al. 2011 Advantage of short regions -> aDNA is already degraded and fragmented Results: V9 - eukaroytes From which phylum/species aDNA can be obtained? • Eukaryotes: • Alveolata Acanthamoeba sp.+ funghi • Rhizaria dominates the assemblage • Stramenopiles (80 %) • Amoebozoa • Opisthokonta Contamination! The first 3 are mostly composed of In situ during the storage planktonics species and cannot come from an ex-situ (storage) contamination Negative Controls -> ok Results: V9 – Planktonic species Planktonic sequences were found at each layer (in green colours) Main planktonic phylum: • Rhizaria (foraminifera + radiolaria) • Alveolata • Archeaplastida • Stramenopiles Results: V4 - diatoms 0 5/20 layers do not amplified. Species: Raphid 100 pennate is present Species Bacteriastrum_elegans throughout the core Chaetoceros_dichatoensis Eucampia_cornuta excepts around glacial Meuniera_membranacea Navicula_cryptotenella Polar−centric−Mediophyceae_X_sp. .Ka. Periods e Pseudo−nitzschia_seriata Ag Raphid−pennate_X_sp. 200 Rhizosolenia_delicatula Skeletonema_ardens Skeletonema_grevillei N. cryptotenella is Skeletonema_menzellii freshwater diatoms, Thalassiosira_mala probably inputs from rivers. The site is 100 km off Sepik river. 300 0 25 50 75 100 Relative proportion Results: planktonic foraminifera 0 5/20 layers do not amplified. 100 Typical assemblages of tropical sites: - warm waters (in Species Candeina nitida Globigerinita glutinata red/orange colours) Globigerinita uvula .Ka. e 200 Globorotalia hirsuta - temperate waters Ag Globorotalia scitula Neogloboquadrina dutertrei (blue colours) Pulleniatina obliquiloculata Some samples are dominated by 300 temperate assemblages, those samples correspond to less warm periods 400 0 50 100 150 Abundance Results: soft-shell foraminifera 0 3/20 layers do not 100 X Species amplified. Aschemonella sp2 CladeA mudball sp CladeC saccaminid sp CladeTIN environmental sp. CladeY allogromid sp Non - fossilized Cylindrogullmia alba Enfor2 Environmental sp. .Ka. e foraminifera 200 Enfor3 Environmental sp. Ag Gloiogullmia sp metabarcodes could Hippocrepina indivisa X Micrometula sp Monothalamea alllogromid sp. be also obtained. Phainogullmia sp Psammophaga sp Tinogullmia sp 300 X 400 0 25 50 75 100 Abundance Conclusion • Could aDNA preserved in cores stored for several years at 4°C storage? and the obtained aDNA is usable? Marine species aDNA was still preserved and could be extracted at almost every layer. Eukaryotes metabarcodes were mostly composed of amoeba. Specific primers for diatoms and foraminifera provide more sequences and assignments until species level. • Core repositories brim with sedimentary cores which if they are intact could be used depending on targeted species. • To target bacteria, funghi, … better use freshly recovered core. Thanks! D622 |EGU2020-17545| BG2.2 Mon, 4 May, 16:15–18:00 .
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