From the Surface Ocean to the Seafloor: Linking Modern and Paleo‐Genetics at the Sabrina Coast, East Antarctica (IN2017_V01)

With ongoing climate change, research into the biological changes occurring in particularly vulnerable ecosystems, such as Antarctica, is critical. The Totten Glacier region, Sabrina Coast, is currently experiencing some of the highest rates of thinning across all East Antarctica. An assessment of the microscopic organisms supporting the ecosystem of the marginal sea‐ice zone over the continental rise is important, yet there is a lack of knowledge about the diversity and distribution of these organisms throughout the water column, and their occurrence and/or preservation in the underlying sediments. Here, we provide a taxonomic overview of the modern and ancient marine bacterial and eukaryotic communities of the Totten Glacier region, using a combination of 16S and 18S rRNA amplicon sequencing (modern DNA) and shotgun metagenomics (sedimentary ancient DNA, sedaDNA). Our data show considerable differences between eukaryote and bacterial signals in the water column versus the sediments. Proteobacteria and diatoms dominate the bacterial and eukaryote composition in the upper water column, while diatoms, dinoflagellates, and haptophytes notably decrease in relative abundance with increasing water depth. Little diatom sedaDNA is preserved in the sediments, which are instead dominated by Proteobacteria and Retaria. We compare the diatom microfossil and sedaDNA record and link the weak preservation of diatom sedaDNA to DNA degradation while sinking through the water column to the seafloor. This study provides the first assessment of DNA transfer from ocean waters to sediments and an overview of the microscopic communities occurring in the climatically important Totten Glacier region.

[1]  Z. Chase,et al.  Unradiogenic reactive phase controls the εNd of authigenic phosphates in East Antarctic margin sediment , 2023, Geochimica et Cosmochimica Acta.

[2]  M. Raymo,et al.  Ancient marine sediment DNA reveals diatom transition in Antarctica , 2022, Nature Communications.

[3]  P. Weatherall,et al.  The International Bathymetric Chart of the Southern Ocean Version 2 , 2022, Scientific Data.

[4]  L. Armbrecht,et al.  An Outlook for the Acquisition of Marine Sedimentary Ancient DNA (sedaDNA) From North Atlantic Ocean Archive Material , 2022, Paleoceanography and Paleoclimatology.

[5]  Tristan Biard Diversity and ecology of Radiolaria in modern oceans , 2022, Environmental microbiology.

[6]  M. Weinbauer,et al.  Reduced bacterial mortality and enhanced viral productivity during sinking in the ocean , 2022, The ISME Journal.

[7]  S. Bertilsson,et al.  Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential , 2022, Environmental microbiology.

[8]  Ellen S. Cameron,et al.  Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities , 2021, Scientific Reports.

[9]  A. Polanowski,et al.  Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems , 2021, PeerJ.

[10]  L. Armbrecht,et al.  Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics , 2021, ISME Communications.

[11]  Corinne Le Quéré,et al.  Climate Change 2013: The Physical Science Basis , 2013 .

[12]  H. Ducklow,et al.  Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula , 2021, Nature Communications.

[13]  M. Bensi,et al.  Water masses distribution offshore the Sabrina Coast ( East Antarctica ) 1 , 2021 .

[14]  A. Marchetti,et al.  Low diversity of a key phytoplankton group along the West Antarctic Peninsula , 2021, Limnology and Oceanography.

[15]  H. Zimmermann,et al.  Sedimentary Ancient DNA From the Subarctic North Pacific: How Sea Ice, Salinity, and Insolation Dynamics Have Shaped Diatom Composition and Richness Over the Past 20,000 Years , 2021, Paleoceanography and Paleoclimatology.

[16]  P. Taberlet,et al.  Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations , 2021, Quaternary.

[17]  G. Hallegraeff,et al.  Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes , 2020, Scientific Reports.

[18]  A. Leventer,et al.  Controls Since the mid‐Pleistocene Transition on Sedimentation and Primary Productivity Downslope of Totten Glacier, East Antarctica , 2020, Paleoceanography and Paleoclimatology.

[19]  J. Pawlowski,et al.  Planktonic foraminifera eDNA signature deposited on the seafloor remains preserved after burial in marine sediments , 2020, Scientific Reports.

[20]  L. Armand,et al.  Scratching the Surface: A Marine Sediment Provenance Record From the Continental Slope of Central Wilkes Land, East Antarctica , 2020, Geochemistry, Geophysics, Geosystems.

[21]  M. Zajączkowski,et al.  Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA , 2020, Scientific Reports.

[22]  R. Romeo,et al.  Continental slope and rise geomorphology seaward of the Totten Glacier, East Antarctica (112°E-122°E) , 2020, Marine Geology.

[23]  E. Bard,et al.  Marine20—The Marine Radiocarbon Age Calibration Curve (0–55,000 cal BP) , 2020, Radiocarbon.

[24]  L. Armbrecht The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems , 2020, Oceanography.

[25]  G. Hallegraeff,et al.  An optimized method for the extraction of ancient eukaryote DNA from marine sediments , 2020, Molecular ecology resources.

[26]  L. Armand,et al.  Upper slope processes and seafloor ecosystems on the Sabrina continental slope, East Antarctica , 2020 .

[27]  Sanghoon Kang,et al.  A Unique Benthic Microbial Community Underlying the Phaeocystis antarctica-Dominated Amundsen Sea Polynya, Antarctica: A Proxy for Assessing the Impact of Global Changes , 2020, Frontiers in Marine Science.

[28]  N. Bindoff,et al.  Antarctic Futures: An Assessment of Climate-Driven Changes in Ecosystem Structure, Function, and Service Provisioning in the Southern Ocean. , 2020, Annual review of marine science.

[29]  Kohske Takahashi,et al.  Welcome to the Tidyverse , 2019, J. Open Source Softw..

[30]  L. Skinner,et al.  Marine Reservoir Age Variability Over the Last Deglaciation: Implications for Marine CarbonCycling and Prospects for Regional Radiocarbon Calibrations , 2019, Paleoceanography and Paleoclimatology.

[31]  Karthik Anantharaman,et al.  Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation , 2019, The ISME Journal.

[32]  Tom O. Delmont,et al.  Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade , 2019, eLife.

[33]  M. V. Ramana Murthy,et al.  A review on the applications and recent advances in environmental DNA (eDNA) metagenomics , 2019, Reviews in Environmental Science and Bio/Technology.

[34]  Yohey Suzuki,et al.  Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation , 2019, Earth-Science Reviews.

[35]  U. Ijaz,et al.  The potential of sedimentary ancient DNA for reconstructing past sea ice evolution , 2019, The ISME Journal.

[36]  Guy D. Williams,et al.  Seasonality of Warm Water Intrusions Onto the Continental Shelf Near the Totten Glacier , 2019, Journal of Geophysical Research: Oceans.

[37]  P. Taberlet,et al.  New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality , 2019, Scientific Reports.

[38]  K. Hinrichs,et al.  Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation , 2019, Scientific Reports.

[39]  Eric Rignot,et al.  Four decades of Antarctic Ice Sheet mass balance from 1979–2017 , 2019, Proceedings of the National Academy of Sciences.

[40]  H. Zimmermann,et al.  Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30,000 years , 2019 .

[41]  D. Fuller,et al.  Neoglacial climate anomalies and the Harappan metamorphosis , 2018, Climate of the Past.

[42]  Erik L. Clarke,et al.  Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments , 2018, bioRxiv.

[43]  Dominique A Cowart,et al.  Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula. , 2017, Marine genomics.

[44]  R. Romeo,et al.  Interactions of the Totten Glacier with the Southern Ocean through multiple glacial cycles (IN2017-V01): Post-survey report , 2018 .

[45]  Janet Kelso,et al.  Neandertal and Denisovan DNA from Pleistocene sediments , 2017, Science.

[46]  D. Boltovskoy Vertical distribution patterns of Radiolaria Polycystina (Protista) in the World Ocean: living ranges, isothermal submersion and settling shells , 2017 .

[47]  S. Giovannoni SAR11 Bacteria: The Most Abundant Plankton in the Oceans. , 2017, Annual review of marine science.

[48]  Lijun He,et al.  Climate oscillations reflected within the microbiome of Arabian Sea sediments , 2016, Scientific Reports.

[49]  Bryan C. Lougheed,et al.  MatCal: Open Source Bayesian 14C Age Calibration in Matlab , 2016 .

[50]  A. Fraser,et al.  Environmental drivers of benthic communities and habitat heterogeneity on an East Antarctic shelf , 2016, Antarctic Science.

[51]  Mark B. Schultz,et al.  Microbial mercury methylation in Antarctic sea ice , 2016, Nature Microbiology.

[52]  N. Mahowald,et al.  Potentially Bioavailable Iron Delivery by Iceberg-hosted Sediments and Atmospheric Dust to the Polar Oceans , 2016 .

[53]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[54]  Daniel H. Huson,et al.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data , 2016, PLoS Comput. Biol..

[55]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[56]  Daniel H. Huson,et al.  MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman , 2016, bioRxiv.

[57]  Kenneth M. Halanych,et al.  Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure , 2016, Front. Microbiol..

[58]  L. Orlando,et al.  AdapterRemoval v2: rapid adapter trimming, identification, and read merging , 2016, BMC Research Notes.

[59]  Luis Pedro Coelho,et al.  Plankton networks driving carbon export in the oligotrophic ocean , 2015, Nature.

[60]  S. Acinas,et al.  Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans , 2015, The ISME Journal.

[61]  B. Scheuchl,et al.  Grounding line retreat of Totten Glacier, East Antarctica, 1996 to 2013 , 2015 .

[62]  H. Tomaru,et al.  Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor , 2015, Science.

[63]  E. Delong,et al.  Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre , 2015, Front. Microbiol..

[64]  B. Legrésy,et al.  Ocean access to a cavity beneath Totten Glacier in East Antarctica , 2015 .

[65]  Eske Willerslev,et al.  Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity , 2015 .

[66]  Robert J. Schmitz,et al.  MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing , 2015, Nature Protocols.

[67]  Philippe Ziegler,et al.  Climate change and Southern Ocean ecosystems I: how changes in physical habitats directly affect marine biota , 2014, Global change biology.

[68]  M. Zajączkowski,et al.  Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium , 2014, Geobiology.

[69]  R. Scherer,et al.  A revised method for determining the absolute abundance of diatoms , 2014, Journal of Paleolimnology.

[70]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[71]  Qi-Long Qin,et al.  Diversity of Both the Cultivable Protease-Producing Bacteria and Bacterial Extracellular Proteases in the Coastal Sediments of King George Island, Antarctica , 2013, PloS one.

[72]  M. Pop,et al.  Robust methods for differential abundance analysis in marker gene surveys , 2013, Nature Methods.

[73]  Matthew Z. DeMaere,et al.  Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics. , 2013, Environmental microbiology.

[74]  T. Williams,et al.  The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. , 2013, Environmental microbiology.

[75]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[76]  Matthew Z. DeMaere,et al.  Global biogeography of SAR11 marine bacteria , 2012, Molecular systems biology.

[77]  F. Not,et al.  Phylogenetic Relationships and Evolutionary Patterns of the Order Collodaria (Radiolaria) , 2012, PloS one.

[78]  G. Hallegraeff,et al.  Climate-driven range expansion of the red-tide dinoflagellate Noctiluca scintillans into the Southern Ocean , 2012 .

[79]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[80]  A. Ishida,et al.  Will krill fare well under Southern Ocean acidification? , 2011, Biology Letters.

[81]  Matthias Meyer,et al.  Illumina sequencing library preparation for highly multiplexed target capture and sequencing. , 2010, Cold Spring Harbor protocols.

[82]  Kevin R. Arrigo,et al.  Coastal Southern Ocean: A strong anthropogenic CO2 sink , 2008 .

[83]  Maria E. Asplund,et al.  Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR , 2008, Applied and Environmental Microbiology.

[84]  Eelco J. Rohling,et al.  High rates of sea-level rise during the last interglacial period , 2008 .

[85]  Lukas H. Meyer,et al.  Summary for Policymakers , 2022, The Ocean and Cryosphere in a Changing Climate.

[86]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[87]  R. Danovaro,et al.  Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems , 2007 .

[88]  P. Legendre,et al.  vegan : Community Ecology Package. R package version 1.8-5 , 2007 .

[89]  S. Giovannoni,et al.  Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom. , 2006, Environmental microbiology.

[90]  B. Jørgensen,et al.  Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[91]  William A. Siebold,et al.  SAR11 clade dominates ocean surface bacterioplankton communities , 2002, Nature.

[92]  A. Abelmann,et al.  Spatial distribution pattern of living polycystine radiolarian taxa — baseline study for paleoenvironmental reconstructions in the Southern Ocean (Atlantic sector) , 1997 .