Articles | Volume 14, issue 11
https://doi.org/10.5194/bg-14-2741-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-14-2741-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
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 Morard
CORRESPONDING AUTHOR
MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
Franck Lejzerowicz
Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
Kate F. Darling
School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FE, UK
School of Geography and GeoSciences, University of St Andrews, Fife, KY16 9AL, UK
Béatrice Lecroq-Bennet
Okinawa Institute of Sciences and Technology Graduate University, 1919-1 Tancha, Onna-son 904-0495, Japan
Mikkel Winther Pedersen
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350K, Denmark
Ludovic Orlando
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350K, Denmark
Jan Pawlowski
Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
Stefan Mulitza
MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
Colomban de Vargas
Centre National de la Recherche Scientifique, UMR7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France
Sorbonne Universités, UPMC Univ Paris 06, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
Michal Kucera
MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
Related authors
Douglas Lessa, Raphaël Morard, Lukas Jonkers, Igor M. Venancio, Runa Reuter, Adrian Baumeister, Ana Luiza Albuquerque, and Michal Kucera
Biogeosciences, 17, 4313–4342, https://doi.org/10.5194/bg-17-4313-2020, https://doi.org/10.5194/bg-17-4313-2020, 2020
Short summary
Short summary
We observed that living planktonic foraminifera had distinct vertically distributed communities across the Subtropical South Atlantic. In addition, a hierarchic alternation of environmental parameters was measured to control the distribution of planktonic foraminifer's species depending on the water depth. This implies that not only temperature but also productivity and subsurface processes are signed in fossil assemblages, which could be used to perform paleoceanographic reconstructions.
Pauline Cornuault, Luc Beaufort, Heiko Pälike, Torsten Bickert, Karl-Heinz Baumann, and Michal Kucera
EGUsphere, https://doi.org/10.5194/egusphere-2025-198, https://doi.org/10.5194/egusphere-2025-198, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
Short summary
Short summary
We present new high-resolution data of the relative contribution of the two main pelagic carbonate producers (coccoliths and foraminifera) to the total pelagic carbonate production from the tropical Atlantic in past warm periods since the Miocene. Our findings suggests that the two groups responded differently to orbital forcing and oceanic changes in tropical ocean, but their proportion changes did not drive the changes in overall pelagic carbonate deposition.
Ewa Demianiuk, Mateusz Baca, Danijela Popović, Inès Barrenechea Angeles, Ngoc-Loi Nguyen, Jan Pawlowski, John B. Anderson, and Wojciech Majewski
EGUsphere, https://doi.org/10.5194/egusphere-2024-2824, https://doi.org/10.5194/egusphere-2024-2824, 2024
Short summary
Short summary
Ancient foraminifera DNA is studied in five Antarctic cores with sediments up to 25 kyr old. We use a standard and a new, more effective marker, which may become the next standard for paleoenvironmental studies. Much less diverse foraminifera occur on slopes of submarine moraines than in open-marine settings. Softly-walled foraminifera, not found in the fossil record, are especially abundant. There is no foraminiferal DNA in tills, suggesting its destruction during glacial redeposition.
Andrea Habura, Stephen P. Alexander, Steven D. Hanes, Andrew J. Gooday, Jan Pawlowski, and Samuel S. Bowser
J. Micropalaeontol., 43, 337–347, https://doi.org/10.5194/jm-43-337-2024, https://doi.org/10.5194/jm-43-337-2024, 2024
Short summary
Short summary
Two species of giant, single-celled "trees” inhabit the seafloor in McMurdo Sound, Antarctica. These unicellular creatures are large enough to be seen and counted by scuba divers. We found that one of the tree species is widely spread, whereas the other inhabits only a small region on the western side of the sound. These types of unicellular trees have not been found elsewhere in the world ocean and are particularly vulnerable to the effects of climate change.
Flor Vermassen, Clare Bird, Tirza M. Weitkamp, Kate F. Darling, Hanna Farnelid, Céline Heuzé, Allison Y. Hsiang, Salar Karam, Christian Stranne, Marcus Sundbom, and Helen K. Coxall
EGUsphere, https://doi.org/10.5194/egusphere-2024-1091, https://doi.org/10.5194/egusphere-2024-1091, 2024
Short summary
Short summary
We provide the first systematic survey of planktonic foraminifera in the high Arctic Ocean. Our results describe the abundance and species composition under summer sea-ice. They indicate that the polar specialist N. pachyderma is the only species present, with subpolar species absent. The dataset will be a valuable reference for continued monitoring of the state of planktonic foraminifera communities as they respond to the ongoing sea-ice decline and the ‘Atlantification’ of the Arctic Ocean.
Peter Köhler and Stefan Mulitza
Clim. Past, 20, 991–1015, https://doi.org/10.5194/cp-20-991-2024, https://doi.org/10.5194/cp-20-991-2024, 2024
Short summary
Short summary
We constructed 160 kyr long mono-specific stacks of δ13C and of δ18O from the wider tropics from the planktic foraminifera G. ruber and/or T. sacculifer and compared them with carbon cycle simulations using the BICYCLE-SE model. In our stacks and our model-based interpretation, we cannot detect a species-specific isotopic fractionation during hard-shell formation as a function of carbonate chemistry in the surrounding seawater, something which is called a carbonate ion effect.
Clare Bird, Kate F. Darling, Rabecca Thiessen, and Anna J. Pieńkowski
EGUsphere, https://doi.org/10.5194/egusphere-2024-497, https://doi.org/10.5194/egusphere-2024-497, 2024
Short summary
Short summary
The polar planktonic foraminifer N. pachyderma eats bacteria and diatoms. Unlike other planktonic species, it also keeps the diatom chloroplasts (photosynthesising organelles) inside its cell. In benthic foraminifera this is known as kleptoplasty, and the roles of these stolen chloroplasts are diverse. Their role in N. pachyderma needs to be investigated to find out if stored chloroplasts enable N. pachyderma to live in polar waters and under the ice where no other planktonic species survive.
Sabrina Hohmann, Michal Kucera, and Anne de Vernal
Clim. Past, 19, 2027–2051, https://doi.org/10.5194/cp-19-2027-2023, https://doi.org/10.5194/cp-19-2027-2023, 2023
Short summary
Short summary
Drivers for dinocyst assemblage compositions differ regionally and through time. Shifts in the assemblages can sometimes only be interpreted robustly by locally and sometimes globally calibrated transfer functions, questioning the reliability of environmental reconstructions. We suggest the necessity of a thorough evaluation of transfer function performance and significance for downcore applications to disclose the drivers for present and fossil dinocyst assemblages in a studied core location.
Michal Kučera and Geert-Jan A. Brummer
J. Micropalaeontol., 42, 33–34, https://doi.org/10.5194/jm-42-33-2023, https://doi.org/10.5194/jm-42-33-2023, 2023
Pauline Cornuault, Thomas Westerhold, Heiko Pälike, Torsten Bickert, Karl-Heinz Baumann, and Michal Kucera
Biogeosciences, 20, 597–618, https://doi.org/10.5194/bg-20-597-2023, https://doi.org/10.5194/bg-20-597-2023, 2023
Short summary
Short summary
We generated high-resolution records of carbonate accumulation rate from the Miocene to the Quaternary in the tropical Atlantic Ocean to characterize the variability in pelagic carbonate production during warm climates. It follows orbital cycles, responding to local changes in tropical conditions, as well as to long-term shifts in climate and ocean chemistry. These changes were sufficiently large to play a role in the carbon cycle and global climate evolution.
Franziska Tell, Lukas Jonkers, Julie Meilland, and Michal Kucera
Biogeosciences, 19, 4903–4927, https://doi.org/10.5194/bg-19-4903-2022, https://doi.org/10.5194/bg-19-4903-2022, 2022
Short summary
Short summary
This study analyses the production of calcite shells formed by one of the main Arctic pelagic calcifiers, the foraminifera N. pachyderma. Using vertically resolved profiles of shell concentration, size and weight, we show that calcification occurs throughout the upper 300 m with an average production flux below the calcification zone of 8 mg CaCO3 m−2 d−1 representing 23 % of the total pelagic biogenic carbonate production. The production flux is attenuated in the twilight zone by dissolution.
Stefan Mulitza, Torsten Bickert, Helen C. Bostock, Cristiano M. Chiessi, Barbara Donner, Aline Govin, Naomi Harada, Enqing Huang, Heather Johnstone, Henning Kuhnert, Michael Langner, Frank Lamy, Lester Lembke-Jene, Lorraine Lisiecki, Jean Lynch-Stieglitz, Lars Max, Mahyar Mohtadi, Gesine Mollenhauer, Juan Muglia, Dirk Nürnberg, André Paul, Carsten Rühlemann, Janne Repschläger, Rajeev Saraswat, Andreas Schmittner, Elisabeth L. Sikes, Robert F. Spielhagen, and Ralf Tiedemann
Earth Syst. Sci. Data, 14, 2553–2611, https://doi.org/10.5194/essd-14-2553-2022, https://doi.org/10.5194/essd-14-2553-2022, 2022
Short summary
Short summary
Stable isotope ratios of foraminiferal shells from deep-sea sediments preserve key information on the variability of ocean circulation and ice volume. We present the first global atlas of harmonized raw downcore oxygen and carbon isotope ratios of various planktonic and benthic foraminiferal species. The atlas is a foundation for the analyses of the history of Earth system components, for finding future coring sites, and for teaching marine stratigraphy and paleoceanography.
Geert-Jan A. Brummer and Michal Kučera
J. Micropalaeontol., 41, 29–74, https://doi.org/10.5194/jm-41-29-2022, https://doi.org/10.5194/jm-41-29-2022, 2022
Short summary
Short summary
To aid researchers working with living planktonic foraminifera, we provide a comprehensive review of names that we consider appropriate for extant species. We discuss the reasons for the decisions we made and provide a list of species and genus-level names as well as other names that have been used in the past but are considered inappropriate for living taxa, stating the reasons.
Lukas Jonkers, Geert-Jan A. Brummer, Julie Meilland, Jeroen Groeneveld, and Michal Kucera
Clim. Past, 18, 89–101, https://doi.org/10.5194/cp-18-89-2022, https://doi.org/10.5194/cp-18-89-2022, 2022
Short summary
Short summary
The variability in the geochemistry among individual foraminifera is used to reconstruct seasonal to interannual climate variability. This method requires that each foraminifera shell accurately records environmental conditions, which we test here using a sediment trap time series. Even in the absence of environmental variability, planktonic foraminifera display variability in their stable isotope ratios that needs to be considered in the interpretation of individual foraminifera data.
Lukas Jonkers, Oliver Bothe, and Michal Kucera
Clim. Past, 17, 2577–2581, https://doi.org/10.5194/cp-17-2577-2021, https://doi.org/10.5194/cp-17-2577-2021, 2021
Julie Meilland, Michael Siccha, Maike Kaffenberger, Jelle Bijma, and Michal Kucera
Biogeosciences, 18, 5789–5809, https://doi.org/10.5194/bg-18-5789-2021, https://doi.org/10.5194/bg-18-5789-2021, 2021
Short summary
Short summary
Planktonic foraminifera population dynamics has long been assumed to be controlled by synchronous reproduction and ontogenetic vertical migration (OVM). Due to contradictory observations, this concept became controversial. We here test it in the Atlantic ocean for four species of foraminifera representing the main clades. Our observations support the existence of synchronised reproduction and OVM but show that more than half of the population does not follow the canonical trajectory.
André Paul, Stefan Mulitza, Rüdiger Stein, and Martin Werner
Clim. Past, 17, 805–824, https://doi.org/10.5194/cp-17-805-2021, https://doi.org/10.5194/cp-17-805-2021, 2021
Short summary
Short summary
Maps and fields of near-sea-surface temperature differences between the past and present can be used to visualize and quantify climate changes and perform simulations with climate models. We used a statistical method to map sparse and scattered data for the Last Glacial Maximum time period (23 000 to 19 000 years before present) to a regular grid. The estimated global and tropical cooling would imply an equilibrium climate sensitivity in the lower to middle part of the currently accepted range.
Markus Raitzsch, Jelle Bijma, Torsten Bickert, Michael Schulz, Ann Holbourn, and Michal Kučera
Clim. Past, 17, 703–719, https://doi.org/10.5194/cp-17-703-2021, https://doi.org/10.5194/cp-17-703-2021, 2021
Short summary
Short summary
At approximately 14 Ma, the East Antarctic Ice Sheet expanded to almost its current extent, but the role of CO2 in this major climate transition is not entirely known. We show that atmospheric CO2 might have varied on 400 kyr cycles linked to the eccentricity of the Earth’s orbit. The resulting change in weathering and ocean carbon cycle affected atmospheric CO2 in a way that CO2 rose after Antarctica glaciated, helping to stabilize the climate system on its way to the “ice-house” world.
Catarina Cavaleiro, Antje H. L. Voelker, Heather Stoll, Karl-Heinz Baumann, and Michal Kucera
Clim. Past, 16, 2017–2037, https://doi.org/10.5194/cp-16-2017-2020, https://doi.org/10.5194/cp-16-2017-2020, 2020
Douglas Lessa, Raphaël Morard, Lukas Jonkers, Igor M. Venancio, Runa Reuter, Adrian Baumeister, Ana Luiza Albuquerque, and Michal Kucera
Biogeosciences, 17, 4313–4342, https://doi.org/10.5194/bg-17-4313-2020, https://doi.org/10.5194/bg-17-4313-2020, 2020
Short summary
Short summary
We observed that living planktonic foraminifera had distinct vertically distributed communities across the Subtropical South Atlantic. In addition, a hierarchic alternation of environmental parameters was measured to control the distribution of planktonic foraminifer's species depending on the water depth. This implies that not only temperature but also productivity and subsurface processes are signed in fossil assemblages, which could be used to perform paleoceanographic reconstructions.
Lukas Jonkers, Olivier Cartapanis, Michael Langner, Nick McKay, Stefan Mulitza, Anne Strack, and Michal Kucera
Earth Syst. Sci. Data, 12, 1053–1081, https://doi.org/10.5194/essd-12-1053-2020, https://doi.org/10.5194/essd-12-1053-2020, 2020
Joanna Pawłowska, Magdalena Łącka, Małgorzata Kucharska, Jan Pawlowski, and Marek Zajączkowski
Clim. Past, 16, 487–501, https://doi.org/10.5194/cp-16-487-2020, https://doi.org/10.5194/cp-16-487-2020, 2020
Short summary
Short summary
Paleoceanographic changes in Storfjorden during the Neoglacial (the last
4000 years) were reconstructed based on microfossil and ancient DNA records. Environmental changes were steered mainly by the interaction between the inflow of Atlantic Water (AW) and sea ice cover. Warming periods were associated with AW inflow and sea ice melting, stimulating primary production. The cold phases were characterized by densely packed sea ice, resulting in limited productivity.
Anna Jentzen, Joachim Schönfeld, Agnes K. M. Weiner, Manuel F. G. Weinkauf, Dirk Nürnberg, and Michal Kučera
J. Micropalaeontol., 38, 231–247, https://doi.org/10.5194/jm-38-231-2019, https://doi.org/10.5194/jm-38-231-2019, 2019
Short summary
Short summary
The study assessed the population dynamics of living planktic foraminifers on a weekly, seasonal, and interannual timescale off the coast of Puerto Rico to improve our understanding of short- and long-term variations. The results indicate a seasonal change of the faunal composition, and over the last decades. Lower standing stocks and lower stable carbon isotope values of foraminifers in shallow waters can be linked to the hurricane Sandy, which passed the Greater Antilles during autumn 2012.
Michael Langner and Stefan Mulitza
Clim. Past, 15, 2067–2072, https://doi.org/10.5194/cp-15-2067-2019, https://doi.org/10.5194/cp-15-2067-2019, 2019
Short summary
Short summary
Collections of paleoclimate data provide valuable information on the functioning of the Earth system but are often difficult to manage due to the inconsistency of data formats and reconstruction methods. We present a software toolbox that combines a simple document-based database with functionality for the visualization and management of marine proxy data. The program allows the efficient homogenization of larger paleoceanographic data sets into quality-controlled and transparent data products.
Mattia Greco, Lukas Jonkers, Kerstin Kretschmer, Jelle Bijma, and Michal Kucera
Biogeosciences, 16, 3425–3437, https://doi.org/10.5194/bg-16-3425-2019, https://doi.org/10.5194/bg-16-3425-2019, 2019
Short summary
Short summary
To be able to interpret the paleoecological signal contained in N. pachyderma's shells, its habitat depth must be known. Our investigation on 104 density profiles of this species from the Arctic and North Atlantic shows that specimens reside closer to the surface when sea-ice and/or surface chlorophyll concentrations are high. This is in contrast with previous investigations that pointed at the position of the deep chlorophyll maximum as the main driver of N. pachyderma vertical distribution.
Haruka Takagi, Katsunori Kimoto, Tetsuichi Fujiki, Hiroaki Saito, Christiane Schmidt, Michal Kucera, and Kazuyoshi Moriya
Biogeosciences, 16, 3377–3396, https://doi.org/10.5194/bg-16-3377-2019, https://doi.org/10.5194/bg-16-3377-2019, 2019
Short summary
Short summary
Photosymbiosis (endosymbiosis with algae) is an evolutionary important ecology for many marine organisms but has poorly been identified among planktonic foraminifera. In this study, we identified and characterized photosymbiosis of various species of planktonic foraminifera by focusing on their photosynthesis–related features. We finally proposed a new framework showing a potential strength of photosymbiosis, which will serve as a basis for future ecological studies of planktonic foraminifera.
Andreia Rebotim, Antje Helga Luise Voelker, Lukas Jonkers, Joanna J. Waniek, Michael Schulz, and Michal Kucera
J. Micropalaeontol., 38, 113–131, https://doi.org/10.5194/jm-38-113-2019, https://doi.org/10.5194/jm-38-113-2019, 2019
Short summary
Short summary
To reconstruct subsurface water conditions using deep-dwelling planktonic foraminifera, we must fully understand how the oxygen isotope signal incorporates into their shell. We report δ18O in four species sampled in the eastern North Atlantic with plankton tows. We assess the size and crust effect on the isotopic δ18O and compared them with predictions from two equations. We reveal different patterns of calcite addition with depth, highlighting the need to perform species-specific calibrations.
Lukas Jonkers and Michal Kučera
Clim. Past, 15, 881–891, https://doi.org/10.5194/cp-15-881-2019, https://doi.org/10.5194/cp-15-881-2019, 2019
Short summary
Short summary
Fossil plankton assemblages have been widely used to reconstruct SST. In such approaches, full taxonomic resolution is often used. We assess whether this is required for reliable reconstructions as some species may not respond to SST. We find that only a few species are needed for low reconstruction errors but that species selection has a pronounced effect on reconstructions. We suggest that the sensitivity of a reconstruction to species pruning can be used as a measure of its robustness.
Charlotte Breitkreuz, André Paul, Stefan Mulitza, Javier García-Pintado, and Michael Schulz
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2019-32, https://doi.org/10.5194/gmd-2019-32, 2019
Publication in GMD not foreseen
Short summary
Short summary
We present a technique for ocean state estimation based on the combination of a simple data assimilation method with a state reduction approach. The technique proves to be very efficient and successful in reducing the model-data misfit and reconstructing a target ocean circulation from synthetic observations. In an application to Last Glacial Maximum proxy data the model-data misfit is greatly reduced but some misfit remains. Two different ocean states are found with similar model-data misfit.
Nadia Al-Sabouni, Isabel S. Fenton, Richard J. Telford, and Michal Kučera
J. Micropalaeontol., 37, 519–534, https://doi.org/10.5194/jm-37-519-2018, https://doi.org/10.5194/jm-37-519-2018, 2018
Short summary
Short summary
In this study we investigate consistency in species-level identifications and whether disagreements are predictable. Overall, 21 researchers from across the globe identified sets of 300 specimens or digital images of planktonic foraminifera. Digital identifications tended to be more disparate. Participants trained by the same person often had more similar identifications. Disagreements hardly affected transfer-function temperature estimates but produced larger differences in diversity metrics.
Jeroen Groeneveld, Helena L. Filipsson, William E. N. Austin, Kate Darling, David McCarthy, Nadine B. Quintana Krupinski, Clare Bird, and Magali Schweizer
J. Micropalaeontol., 37, 403–429, https://doi.org/10.5194/jm-37-403-2018, https://doi.org/10.5194/jm-37-403-2018, 2018
Short summary
Short summary
Current climate and environmental changes strongly affect shallow marine and coastal areas like the Baltic Sea. The combination of foraminiferal geochemistry and environmental parameters demonstrates that in a highly variable setting like the Baltic Sea, it is possible to separate different environmental impacts on the foraminiferal assemblages and therefore use chemical factors to reconstruct how seawater temperature, salinity, and oxygen varied in the past and may vary in the future.
Kerstin Kretschmer, Lukas Jonkers, Michal Kucera, and Michael Schulz
Biogeosciences, 15, 4405–4429, https://doi.org/10.5194/bg-15-4405-2018, https://doi.org/10.5194/bg-15-4405-2018, 2018
Short summary
Short summary
The fossil shells of planktonic foraminifera are widely used to reconstruct past climate conditions. To do so, information about their seasonal and vertical habitat is needed. Here we present an updated version of a planktonic foraminifera model to better understand species-specific habitat dynamics under climate change. This model produces spatially and temporally coherent distribution patterns, which agree well with available observations, and can thus aid the interpretation of proxy records.
Rike Völpel, André Paul, Annegret Krandick, Stefan Mulitza, and Michael Schulz
Geosci. Model Dev., 10, 3125–3144, https://doi.org/10.5194/gmd-10-3125-2017, https://doi.org/10.5194/gmd-10-3125-2017, 2017
Short summary
Short summary
This study presents the implementation of stable water isotopes in the MITgcm and describes the results of an equilibrium simulation under pre-industrial conditions. The model compares well to observational data and measurements of plankton tow records and thus opens wide prospects for long-term simulations in a paleoclimatic context.
Lukas Jonkers and Michal Kučera
Clim. Past, 13, 573–586, https://doi.org/10.5194/cp-13-573-2017, https://doi.org/10.5194/cp-13-573-2017, 2017
Short summary
Short summary
Planktonic foraminifera – the most important proxy carriers in palaeoceanography – adjust their seasonal and vertical habitat. They are thought to do so in a way that minimises the change in their environment, implying that proxy records based on these organisms may not capture the full amplitude of past climate change. Here we demonstrate that they indeed track a particular thermal habitat and suggest that this could lead to a 40 % underestimation of reconstructed temperature change.
Philipp M. Munz, Stephan Steinke, Anna Böll, Andreas Lückge, Jeroen Groeneveld, Michal Kucera, and Hartmut Schulz
Clim. Past, 13, 491–509, https://doi.org/10.5194/cp-13-491-2017, https://doi.org/10.5194/cp-13-491-2017, 2017
Short summary
Short summary
We present the results of several independent proxies of summer SST and upwelling SST from the Oman margin indicative of monsoon strength during the early Holocene. In combination with indices of carbonate preservation and bottom water redox conditions, we demonstrate that a persistent solar influence was modulating summer monsoon intensity. Furthermore, bottom water conditions are linked to atmospheric forcing, rather than changes of intermediate water masses.
Shuwen Sun, Enno Schefuß, Stefan Mulitza, Cristiano M. Chiessi, André O. Sawakuchi, Matthias Zabel, Paul A. Baker, Jens Hefter, and Gesine Mollenhauer
Biogeosciences, 14, 2495–2512, https://doi.org/10.5194/bg-14-2495-2017, https://doi.org/10.5194/bg-14-2495-2017, 2017
Clare Bird, Kate F. Darling, Ann D. Russell, Catherine V. Davis, Jennifer Fehrenbacher, Andrew Free, Michael Wyman, and Bryne T. Ngwenya
Biogeosciences, 14, 901–920, https://doi.org/10.5194/bg-14-901-2017, https://doi.org/10.5194/bg-14-901-2017, 2017
Short summary
Short summary
Accurate ecological data on planktic foraminifera (calcifying microbes that play an important role in the carbon cycle) are important for modelling their response to climate change. We studied the species G. bulloides. A lack of algal symbionts and unusual shell chemistry suggest a different life history compared to other spinose species. We demonstrate that G. bulloides hosts cyanobacterial endobionts. This has implications for modelling this species and for understanding its shell chemistry.
Andreia Rebotim, Antje H. L. Voelker, Lukas Jonkers, Joanna J. Waniek, Helge Meggers, Ralf Schiebel, Igaratza Fraile, Michael Schulz, and Michal Kucera
Biogeosciences, 14, 827–859, https://doi.org/10.5194/bg-14-827-2017, https://doi.org/10.5194/bg-14-827-2017, 2017
Short summary
Short summary
Planktonic foraminifera species depth habitat remains poorly constrained and the existing conceptual models are not sufficiently tested by observational data. Here we present a synthesis of living planktonic foraminifera abundance data in the subtropical eastern North Atlantic from vertical plankton tows. We also test potential environmental factors influencing the species depth habitat and investigate yearly or lunar migration cycles. These findings may impact paleoceanographic studies.
Joanna Pawłowska, Marek Zajączkowski, Magdalena Łącka, Franck Lejzerowicz, Philippe Esling, and Jan Pawlowski
Clim. Past, 12, 1459–1472, https://doi.org/10.5194/cp-12-1459-2016, https://doi.org/10.5194/cp-12-1459-2016, 2016
Short summary
Short summary
The presented study focuses on the last millennium of the palaeoclimatic history of Svalbard region. The investigation was based on classical palaeoceanographic proxies, strengthened by the analysis of ancient foraminiferal DNA in down-core sediment samples. This study is the first attempt to implement the aDNA record in the palaeoenvironmental reconstruction. The aDNA data revealed even small environmetal changes that were not evidenced in the sedimentological and micropalaeontological record.
L. Jonkers and M. Kučera
Biogeosciences, 12, 2207–2226, https://doi.org/10.5194/bg-12-2207-2015, https://doi.org/10.5194/bg-12-2207-2015, 2015
I. Hessler, S. P. Harrison, M. Kucera, C. Waelbroeck, M.-T. Chen, C. Anderson, A. de Vernal, B. Fréchette, A. Cloke-Hayes, G. Leduc, and L. Londeix
Clim. Past, 10, 2237–2252, https://doi.org/10.5194/cp-10-2237-2014, https://doi.org/10.5194/cp-10-2237-2014, 2014
A. J. Enge, U. Witte, M. Kucera, and P. Heinz
Biogeosciences, 11, 2017–2026, https://doi.org/10.5194/bg-11-2017-2014, https://doi.org/10.5194/bg-11-2017-2014, 2014
M. F. G. Weinkauf, T. Moller, M. C. Koch, and M. Kučera
Biogeosciences, 10, 6639–6655, https://doi.org/10.5194/bg-10-6639-2013, https://doi.org/10.5194/bg-10-6639-2013, 2013
Y. Milker, R. Rachmayani, M. F. G. Weinkauf, M. Prange, M. Raitzsch, M. Schulz, and M. Kučera
Clim. Past, 9, 2231–2252, https://doi.org/10.5194/cp-9-2231-2013, https://doi.org/10.5194/cp-9-2231-2013, 2013
J. A. Collins, A. Govin, S. Mulitza, D. Heslop, M. Zabel, J. Hartmann, U. Röhl, and G. Wefer
Clim. Past, 9, 1181–1191, https://doi.org/10.5194/cp-9-1181-2013, https://doi.org/10.5194/cp-9-1181-2013, 2013
R. J. Telford, C. Li, and M. Kucera
Clim. Past, 9, 859–870, https://doi.org/10.5194/cp-9-859-2013, https://doi.org/10.5194/cp-9-859-2013, 2013
Related subject area
Biodiversity and Ecosystem Function: Paleo
Palaeoecology of ungulates in northern Iberia during the Late Pleistocene through isotopic analysis of teeth
Reply to Head's comment on “The Volyn biota (Ukraine) – indications of 1.5 Gyr old eukaryotes in 3D preservation, a spotlight on the `boring billion' ” by Franz et al. (2023)
Occupancy history influences extinction risk of fossil marine microplankton groups
Mire edge is not a marginal thing: Assessing the factors behind the formation, vegetation succession, and carbon balance of a subarctic fen margin
Comment on “The Volyn biota (Ukraine) – indications of 1.5 Gyr old eukaryotes in 3D preservation, a spotlight on the `boring billion' ” by Franz et al. (2023)
Rates of palaeoecological change can inform ecosystem restoration
Paleoecology and evolutionary response of planktonic foraminifera to the mid-Pliocene Warm Period and Plio-Pleistocene bipolar ice sheet expansion
Late Neogene evolution of modern deep-dwelling plankton
Photosynthetic activity in Devonian Foraminifera
Microbial activity, methane production, and carbon storage in Early Holocene North Sea peats
Ecosystem regimes and responses in a coupled ancient lake system from MIS 5b to present: the diatom record of lakes Ohrid and Prespa
Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions
Differential resilience of ancient sister lakes Ohrid and Prespa to environmental disturbances during the Late Pleistocene
Stable isotope study of a new chondrichthyan fauna (Kimmeridgian, Porrentruy, Swiss Jura): an unusual freshwater-influenced isotopic composition for the hybodont shark Asteracanthus
Amelioration of marine environments at the Smithian–Spathian boundary, Early Triassic
Weathering by tree-root-associating fungi diminishes under simulated Cenozoic atmospheric CO2 decline
The impact of land-use change on floristic diversity at regional scale in southern Sweden 600 BC–AD 2008
Climate-related changes in peatland carbon accumulation during the last millennium
Stratigraphy and paleoenvironments of the early to middle Holocene Chipalamawamba Beds (Malawi Basin, Africa)
Experimental mineralization of crustacean eggs: new implications for the fossilization of Precambrian–Cambrian embryos
The last glacial-interglacial cycle in Lake Ohrid (Macedonia/Albania): testing diatom response to climate
Mónica Fernández-García, Sarah Pederzani, Kate Britton, Lucía Agudo-Pérez, Andrea Cicero, Jeanne Marie Geiling, Joan Daura, Montserrat Sanz, and Ana B. Marín-Arroyo
Biogeosciences, 21, 4413–4437, https://doi.org/10.5194/bg-21-4413-2024, https://doi.org/10.5194/bg-21-4413-2024, 2024
Short summary
Short summary
Significant climatic changes affected Europe's vegetation and fauna, affecting human subsistence strategies during the Late Pleistocene. Reconstructing the local conditions humans faced is essential to understanding their adaptation processes and resilience. This study analyses the chemical composition of the teeth of herbivores consumed by humans 80,000 to 15,000 years ago, revealing the ecology of ungulates in northern Iberia and thus the palaeoenvironment humans exploited.
Gerhard Franz, Vladimir Khomenko, Peter Lyckberg, Vsevolod Chournousenko, and Ulrich Struck
Biogeosciences, 21, 4119–4131, https://doi.org/10.5194/bg-21-4119-2024, https://doi.org/10.5194/bg-21-4119-2024, 2024
Short summary
Short summary
The Volyn biota (Ukraine), previously assumed to be an extreme case of natural abiotic synthesis of organic matter, is more likely a diverse assemblage of fossils from the deep biosphere. Although contamination by modern organisms cannot completely be ruled out, it is unlikely, considering all aspects, i.e., their mode of occurrence in the deep biosphere, their fossilization and mature state of organic matter, their isotope signature, and their large morphological diversity.
Isaiah E. Smith, Ádám T. Kocsis, and Wolfgang Kiessling
EGUsphere, https://doi.org/10.5194/egusphere-2024-2597, https://doi.org/10.5194/egusphere-2024-2597, 2024
Short summary
Short summary
We examine how change in a species' range size over time influences that species' extinction risk. We analyze the interaction of instantaneous range size, range size change, and fossil sampling, and how these terms relate to extinction risk in marine microplankton. We find that the change in geographic range is the most informative predictor of extinction among the three examined variables. Using predictive models, we also assess extinction probability in four extant groups.
Teemu Juselius-Rajamäki, Sanna Piilo, Susanna Salminen-Paatero, Emilia Tuomaala, Tarmo Virtanen, Atte Korhola, Anna Autio, Hannu Marttila, Pertti Ala-Aho, Annalea Lohila, and Minna Väliranta
EGUsphere, https://doi.org/10.5194/egusphere-2024-2102, https://doi.org/10.5194/egusphere-2024-2102, 2024
Short summary
Short summary
The vegetation can be used to infer the potential climate feedback of peatlands. New studies have shown recent expansion of peatlands but their plant community succession of has not been studied. Although generally described as dry bog-types, our results show that peatland margins in a subarctic fen initiated as wet fen with high methane emissions and shifted to dryer peatland types only after dryer post Little Ice Age climate. Thus, they have acted as a carbon source for most of their history.
Martin J. Head, James B. Riding, Jennifer M. K. O'Keefe, Julius Jeiter, and Julia Gravendyck
Biogeosciences, 21, 1773–1783, https://doi.org/10.5194/bg-21-1773-2024, https://doi.org/10.5194/bg-21-1773-2024, 2024
Short summary
Short summary
A diverse suite of “fossils” associated with the ~1.5 Ga Volyn (Ukraine) kerite was published recently. We show that at least some of them represent modern contamination including plant hairs, pollen, and likely later fungal growth. Comparable diversity is shown to exist in moderm museum dust, calling into question whether any part of the Volyn biota is of biological origin while emphasising the need for scrupulous care in collecting, analysing, and identifying Precambrian microfossils.
Walter Finsinger, Christian Bigler, Christoph Schwörer, and Willy Tinner
Biogeosciences, 21, 1629–1638, https://doi.org/10.5194/bg-21-1629-2024, https://doi.org/10.5194/bg-21-1629-2024, 2024
Short summary
Short summary
Rate-of-change records based on compositional data are ambiguous as they may rise irrespective of the underlying trajectory of ecosystems. We emphasize the importance of characterizing both the direction and the rate of palaeoecological changes in terms of key features of ecosystems rather than solely on community composition. Past accelerations of community transformation may document the potential of ecosystems to rapidly recover important ecological attributes and functions.
Adam Woodhouse, Frances A. Procter, Sophie L. Jackson, Robert A. Jamieson, Robert J. Newton, Philip F. Sexton, and Tracy Aze
Biogeosciences, 20, 121–139, https://doi.org/10.5194/bg-20-121-2023, https://doi.org/10.5194/bg-20-121-2023, 2023
Short summary
Short summary
This study looked into the regional and global response of planktonic foraminifera to the climate over the last 5 million years, when the Earth cooled significantly. These single celled organisms exhibit the best fossil record available to science. We document an abundance switch from warm water to cold water species as the Earth cooled. Moreover, a closer analysis of certain species may indicate higher fossil diversity than previously thought, which has implications for evolutionary studies.
Flavia Boscolo-Galazzo, Amy Jones, Tom Dunkley Jones, Katherine A. Crichton, Bridget S. Wade, and Paul N. Pearson
Biogeosciences, 19, 743–762, https://doi.org/10.5194/bg-19-743-2022, https://doi.org/10.5194/bg-19-743-2022, 2022
Short summary
Short summary
Deep-living organisms are a major yet poorly known component of ocean biomass. Here we reconstruct the evolution of deep-living zooplankton and phytoplankton. Deep-dwelling zooplankton and phytoplankton did not occur 15 Myr ago, when the ocean was several degrees warmer than today. Deep-dwelling species first evolve around 7.5 Myr ago, following global climate cooling. Their evolution was driven by colder ocean temperatures allowing more food, oxygen, and light at depth.
Zofia Dubicka, Maria Gajewska, Wojciech Kozłowski, Pamela Hallock, and Johann Hohenegger
Biogeosciences, 18, 5719–5728, https://doi.org/10.5194/bg-18-5719-2021, https://doi.org/10.5194/bg-18-5719-2021, 2021
Short summary
Short summary
Benthic foraminifera play a significant role in modern reefal ecosystems mainly due to their symbiosis with photosynthetic microorganisms. Foraminifera were also components of Devonian stromatoporoid coral reefs; however, whether they could have harbored symbionts has remained unclear. We show that Devonian foraminifera may have stayed photosynthetically active, which likely had an impact on their evolutionary radiation and possibly also on the functioning of Paleozoic shallow marine ecosystems.
Tanya J. R. Lippmann, Michiel H. in 't Zandt, Nathalie N. L. Van der Putten, Freek S. Busschers, Marc P. Hijma, Pieter van der Velden, Tim de Groot, Zicarlo van Aalderen, Ove H. Meisel, Caroline P. Slomp, Helge Niemann, Mike S. M. Jetten, Han A. J. Dolman, and Cornelia U. Welte
Biogeosciences, 18, 5491–5511, https://doi.org/10.5194/bg-18-5491-2021, https://doi.org/10.5194/bg-18-5491-2021, 2021
Short summary
Short summary
This paper is a step towards understanding the basal peat ecosystem beneath the North Sea. Plant remains followed parallel sequences. Methane concentrations were low with local exceptions, with the source likely being trapped pockets of millennia-old methane. Microbial community structure indicated the absence of a biofilter and was diverse across sites. Large carbon stores in the presence of methanogens and in the absence of methanotrophs have the potential to be metabolized into methane.
Aleksandra Cvetkoska, Elena Jovanovska, Alexander Francke, Slavica Tofilovska, Hendrik Vogel, Zlatko Levkov, Timme H. Donders, Bernd Wagner, and Friederike Wagner-Cremer
Biogeosciences, 13, 3147–3162, https://doi.org/10.5194/bg-13-3147-2016, https://doi.org/10.5194/bg-13-3147-2016, 2016
Elizaveta Rivkina, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin, Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov
Biogeosciences, 13, 2207–2219, https://doi.org/10.5194/bg-13-2207-2016, https://doi.org/10.5194/bg-13-2207-2016, 2016
Short summary
Short summary
A comparative analysis of the metagenomes from two 30,000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which are characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed both a low abundance of methanogenic archaea and enzymes from the carbon, nitrogen, and sulfur cycles.
Elena Jovanovska, Aleksandra Cvetkoska, Torsten Hauffe, Zlatko Levkov, Bernd Wagner, Roberto Sulpizio, Alexander Francke, Christian Albrecht, and Thomas Wilke
Biogeosciences, 13, 1149–1161, https://doi.org/10.5194/bg-13-1149-2016, https://doi.org/10.5194/bg-13-1149-2016, 2016
L. Leuzinger, L. Kocsis, J.-P. Billon-Bruyat, S. Spezzaferri, and T. Vennemann
Biogeosciences, 12, 6945–6954, https://doi.org/10.5194/bg-12-6945-2015, https://doi.org/10.5194/bg-12-6945-2015, 2015
Short summary
Short summary
We measured the oxygen isotopic composition of Late Jurassic chondrichthyan teeth (sharks, rays, chimaeras) from the Swiss Jura to get ecological information. The main finding is that the extinct shark Asteracanthus (Hybodontiformes) could inhabit reduced salinity areas, although previous studies on other European localities always resulted in a clear marine isotopic signal for this genus. We propose a mainly marine ecology coupled with excursions into areas of lower salinity in our study site.
L. Zhang, L. Zhao, Z.-Q. Chen, T. J. Algeo, Y. Li, and L. Cao
Biogeosciences, 12, 1597–1613, https://doi.org/10.5194/bg-12-1597-2015, https://doi.org/10.5194/bg-12-1597-2015, 2015
Short summary
Short summary
The Smithian--Spathian boundary was a key event in the recovery of marine environments and ecosystems following the end-Permian mass extinction ~1.5 million years earlier. Our analysis of the Shitouzhai section in South China reveals major changes in oceanographic conditions at the SSB intensification of oceanic circulation leading to enhanced upwelling of nutrient- and sulfide-rich deep waters and coinciding with an abrupt cooling that terminated the Early Triassic hothouse climate.
J. Quirk, J. R. Leake, S. A. Banwart, L. L. Taylor, and D. J. Beerling
Biogeosciences, 11, 321–331, https://doi.org/10.5194/bg-11-321-2014, https://doi.org/10.5194/bg-11-321-2014, 2014
D. Fredh, A. Broström, M. Rundgren, P. Lagerås, F. Mazier, and L. Zillén
Biogeosciences, 10, 3159–3173, https://doi.org/10.5194/bg-10-3159-2013, https://doi.org/10.5194/bg-10-3159-2013, 2013
D. J. Charman, D. W. Beilman, M. Blaauw, R. K. Booth, S. Brewer, F. M. Chambers, J. A. Christen, A. Gallego-Sala, S. P. Harrison, P. D. M. Hughes, S. T. Jackson, A. Korhola, D. Mauquoy, F. J. G. Mitchell, I. C. Prentice, M. van der Linden, F. De Vleeschouwer, Z. C. Yu, J. Alm, I. E. Bauer, Y. M. C. Corish, M. Garneau, V. Hohl, Y. Huang, E. Karofeld, G. Le Roux, J. Loisel, R. Moschen, J. E. Nichols, T. M. Nieminen, G. M. MacDonald, N. R. Phadtare, N. Rausch, Ü. Sillasoo, G. T. Swindles, E.-S. Tuittila, L. Ukonmaanaho, M. Väliranta, S. van Bellen, B. van Geel, D. H. Vitt, and Y. Zhao
Biogeosciences, 10, 929–944, https://doi.org/10.5194/bg-10-929-2013, https://doi.org/10.5194/bg-10-929-2013, 2013
B. Van Bocxlaer, W. Salenbien, N. Praet, and J. Verniers
Biogeosciences, 9, 4497–4512, https://doi.org/10.5194/bg-9-4497-2012, https://doi.org/10.5194/bg-9-4497-2012, 2012
D. Hippler, N. Hu, M. Steiner, G. Scholtz, and G. Franz
Biogeosciences, 9, 1765–1775, https://doi.org/10.5194/bg-9-1765-2012, https://doi.org/10.5194/bg-9-1765-2012, 2012
J. M. Reed, A. Cvetkoska, Z. Levkov, H. Vogel, and B. Wagner
Biogeosciences, 7, 3083–3094, https://doi.org/10.5194/bg-7-3083-2010, https://doi.org/10.5194/bg-7-3083-2010, 2010
Cited articles
Adams, R. I., Amend, A. S., Taylor, J. W., and Bruns, T. D.: A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: A Case Study of Fungi in Indoor Dust, Microb. Ecol., 66, 735–741, https://doi.org/10.1007/s00248-013-0266-4, 2013a.
Adams, R. I., Miletto, M., Taylor, J. W., and Bruns, T. D.: Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances, ISME J., 7, 1262–1273, https://doi.org/10.1038/ismej.2013.28, 2013b.
Adl, S. M., Simpson, A. G. B., Lane, C. E., Lukeš, J., Bass, D., Bowser, S. S., Brown, M. W., Burki, F., Dunthorn, M., Hampl, V., Heiss, A., Hoppenrath, M., Lara, E., Le Gall, L., Lynn, D. H., McManus, H., Mitchell, E. a D., Mozley-Stanridge, S. E., Parfrey, L. W., Pawlowski, J., Rueckert, S., Shadwick, R. S., Shadwick, L., Schoch, C. L., Smirnov, A., and Spiegel, F. W.: The revised classification of eukaryotes, J. Eukaryot. Microbiol., 59, 429–93, https://doi.org/10.1111/j.1550-7408.2012.00644.x, 2012.
Aurahs, R., Göker, M., Grimm, G. W., Hemleben, V., Hemleben, C., Schiebel, R., and Kucera, M.: Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences, Bioinform. Biol. Insights, 3, 155–177, 2009.
Berger, W. H. and Parker, F. L.: Diversity of planktonic foraminifera in deep-sea sediments, Science, 168, 1345–1347, https://doi.org/10.1126/science.168.3937.1345, 1970.
Boere, A. C., Rijpstra, W. I. C., De Lange, G. J., Sinninghe Damsté, J. S., and Coolen, M. J. L.: Preservation potential of ancient plankton DNA in Pleistocene marine sediments, Geobiology, 9, 377–393, https://doi.org/10.1111/j.1472-4669.2011.00290.x, 2011.
Bradley, I. M., Pinto, A. J., and Guest, J. S.: Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities, edited by G. Voordouw, Appl. Environ. Microbiol., 82, 5878–5891, https://doi.org/10.1128/AEM.01630-16, 2016.
Brummer, G. A., Hemleben, C., and Michael, S.: Planktonic foraminiferal ontogeny and new perspectives for micropalaeontology, Nature, 319, 50–52, 1986.
Capo, E., Debroas, D., Arnaud, F., and Domaizon, I.: Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity, Microb. Ecol., 70, 865–875, https://doi.org/10.1007/s00248-015-0627-2, 2015.
Ceccherini, M. T., Ascher, J., Agnelli, A., Borgogni, F., Pantani, O. L., and Pietramellara, G.: Experimental discrimination and molecular characterization of the extracellular soil DNA fraction, Antonie Van Leeuwenhoek, 96, 653–657, https://doi.org/10.1007/s10482-009-9354-3, 2009.
Coolen, M. J. L. and Overmann, J.: 217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment, Environ. Microbiol., 9, 238–249, https://doi.org/10.1111/j.1462-2920.2006.01134.x, 2007.
Coolen, M. J. L., Saenz, J. P., Giosan, L., Trowbridge, N. Y., Dimitrov, P., Dimitrov, D., and Eglinton, T. I.: DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene, Earth Planet. Sc. Lett., 284, 610–621, https://doi.org/10.1016/j.epsl.2009.05.029, 2009.
Coolen, M. J. L., Orsi, W. D., Balkema, C., Quince, C., Harris, K., Sylva, S. P., Filipova-Marinova, M., and Giosan, L.: Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene, P. Natl. Acad. Sci. USA, 110, 8609–14, https://doi.org/10.1073/pnas.1219283110, 2013.
Corinaldesi, C., Dell'Anno, A., and Danovaro, R.: Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems, Limnol. Oceanogr., 52, 508–516, https://doi.org/10.4319/lo.2007.52.2.0508, 2007.
Corinaldesi, C., Barucca, M., Luna, G. M., and Dell'Anno, A.: Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments, Mol. Ecol., 20, 642–54, https://doi.org/10.1111/j.1365-294X.2010.04958.x, 2011.
Corinaldesi, C., Tangherlini, M., Luna, G. M., and Anno, A. D.: Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins, P. R. Soc. B, 281, 1–10, https://doi.org/10.1098/rspb.2013.3299, 2014.
Darling, K. F. and Wade, C. M.: The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes, Mar. Micropaleontol., 67, 216–238, https://doi.org/10.1016/j.marmicro.2008.01.009, 2008.
Dell'Anno, A. and Danovaro, R.: Extracellular DNA Plays a Key Role in Deep-Sea Ecosystem Functioning, Science, 309, 2179–2179, https://doi.org/10.1126/science.1117475, 2005.
de Vargas, C., Zaninetti, L., Hilbrecht, H., and Pawlowski, J.: Phylogeny and rates of molecular evolution of planktonic foraminifera: SSU rDNA sequences compared to the fossil record, J. Mol. Evol., 45, 285–294, 1997.
de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahe, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horak, A., Jaillon, O., Lima-Mendez, G., Luke, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., Karsenti, E., Boss, E., Follows, M., Karp-Boss, L., Krzic, U., Reynaud, E. G., Sardet, C., Sullivan, M. B., and Velayoudon, D.: Eukaryotic plankton diversity in the sunlit ocean, Science, 348, 1261605–1261605, https://doi.org/10.1126/science.1261605, 2015.
Dutkiewicz, A., O'Callaghan, S., and Müller, R. D.: Controls on the distribution of deep-sea sediments, Geochem. Geophy. Geosy., 17, 3075–3098, https://doi.org/10.1002/2016GC006428, 2016.
Esling, P., Lejzerowicz, F., and Pawlowski, J.: Accurate multiplexing and filtering for high-throughput amplicon-sequencing, Nucl. Acid. Res., 43, 2513–2524, https://doi.org/10.1093/nar/gkv107, 2015.
Gouy, M., Guindon, S., and Gascuel, O.: SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol., 27, 221–4, https://doi.org/10.1093/molbev/msp259, 2010.
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J. R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H. C. F., Lara, E., Le Bescot, N., Logares, R., Mahe, F., Massana, R., Montresor, M., Morard, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A.-L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P., and Christen, R.: The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucl. Acid. Res., 41, D597–D604, https://doi.org/10.1093/nar/gks1160, 2013.
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O.: New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0, Syst. Biol., 59, 307–321, https://doi.org/10.1093/sysbio/syq010, 2010.
Hammer, Ø., Harper, D. A. T., and Ryan, P. D.: Paleontological statistics software package for education and data analysis, Palaeontol. Electron., 4, 9–18, https://doi.org/10.1016/j.bcp.2008.05.025, 2001.
Hemleben, C., Michael, S., and Anderson, O. R.: Modern Planktonic Foraminifera, Springer-Verlarg, New York, 1989.
Hillaire-Marcel, C. and de Vernal, A.: Proxies in Late Cenozoic Paleoceanography, Elsevier, 2007.
Katoh, K. and Standley, D. M.: MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol., 30, 772–780, https://doi.org/10.1093/molbev/mst010, 2013.
Kirkpatrick, J. B., Walsh, E. A., and D'Hondt, S.: Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales, Geology, 44, 615–618, https://doi.org/10.1130/G37933.1, 2016.
Kucera, M., Weinelt, M., Kiefer, T., Pflaumann, U., Hayes, A., Weinelt, M., Chen, M.-T., Mix, A. C., Barrows, T. T., Cortijo, E., Duprat, J., Juggins, S., and Waelbroeck, C.: Reconstruction of sea-surface temperatures from assemblages of planktonic foraminifera: multi-technique approach based on geographically constrained calibration data sets and its application to glacial Atlantic and Pacific Oceans, Quaternary Sci. Rev., 24, 951–998, https://doi.org/10.1016/j.quascirev.2004.07.014, 2005.
Lecroq, B., Lejzerowicz, F., Bachar, D., Christen, R., Esling, P., Baerlocher, L., Osterås, M., Farinelli, L., and Pawlowski, J.: Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments, P. Natl. Acad. Sci. USA, 108, 13177–13182, https://doi.org/10.1073/pnas.1018426108, 2011.
Lejzerowicz, F., Esling, P., Majewski, W., Szczucinski, W., Decelle, J., Obadia, C., Arbizu, P. M., and Pawlowski, J.: Ancient DNA complements microfossil record in deep-sea subsurface sediments, Biol. Lett., 9, 20130283–20130283, https://doi.org/10.1098/rsbl.2013.0283, 2013.
Letunic, I. and Bork, P.: Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucl. Acid. Res., 39, W475–W478, https://doi.org/10.1093/nar/gkr201, 2011.
Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., D'Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sanchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., and Raes, J.: Determinants of community structure in the global plankton interactome, Science, 348, 1262073–1262073, https://doi.org/10.1126/science.1262073, 2015.
Morard, R., Darling, K. F., Mahé, F., Audic, S., Ujiié, Y., Weiner, A. K. M., André, A., Seears, H. a., Wade, C. M., Quillévéré, F., Douady, C. J., Escarguel, G., de Garidel-Thoron, T., Siccha, M., Kucera, M., and de Vargas, C.: PFR2: a curated database of planktonic Foraminifera18S ribosomal DNA as a resource for studies of plankton ecology, biogeography, and evolution, Mol. Ecol. Resour., 49, 1–14, https://doi.org/10.1111/1755-0998.12410, 2015.
Morard, R., Escarguel, G., Weiner, A. K. M., André, A., Douady, C. J., Wade, C. M., Darling, K. F., Ujiié, Y., Seears, H. A., Quillévéré, F., de Garidel-Thoron, T., de Vargas, C., and Kucera, M.: Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera, Syst. Biol., 65, 925–940, https://doi.org/10.1093/sysbio/syw031, 2016.
Paulson, J. N., Stine, O. C., Bravo, H. C., and Pop, M.: Differential abundance analysis for microbial marker-gene surveys, Nat. Methods, 10, 1200–1202, https://doi.org/10.1038/nmeth.2658, 2013.
Needleman, S. B. and Wunsch, C. D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol., 48, 443–453, 1970.
Pawłowska, J., Lejzerowicz, F., Esling, P., Szczuciński, W., Zajączkowski, M., and Pawlowski, J.: Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium, Geobiology, 12, 277–88, https://doi.org/10.1111/gbi.12087, 2014.
Pawlowski, J. and Lecroq, B.: Short rDNA barcodes for species identification in foraminifera, J. Eukaryot. Microbiol., 57, 197–205, https://doi.org/10.1111/j.1550-7408.2009.00468.x, 2010.
Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., Bowser, S. S., Cepicka, I., Decelle, J., Dunthorn, M., Fiore-Donno, A. M., Gile, G. H., Holzmann, M., Jahn, R., Jirků, M., Keeling, P. J., Kostka, M., Kudryavtsev, A., Lara, E., Lukeš, J., Mann, D. G., Mitchell, E. a D., Nitsche, F., Romeralo, M., Saunders, G. W., Simpson, A. G. B., Smirnov, A. V, Spouge, J. L., Stern, R. F., Stoeck, T., Zimmermann, J., Schindel, D., and de Vargas, C.: CBOL Protist Working Group: Barcoding Eukaryotic richness beyond the Animal, Plant, and Fungal Kingdoms, PLoS Biol., 10, e1001419, https://doi.org/10.1371/journal.pbio.1001419, 2012.
Pawlowski, J., Esling, P., Lejzerowicz, F., Cedhagen, T., and Wilding, T. A.: Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities, Mol. Ecol. Resour., 14, 1129–1140, https://doi.org/10.1111/1755-0998.12261, 2014a.
Pawlowski, J., Lejzerowicz, F. ,and Esling, P.: Next-Generation Environmental Diversity Surveys of Foraminifera?: Preparing the Future, Biol. Bull., 227, 93–106, 2014b.
Paulson, J. N., Pop, M., and Bravo, H. C.: metagenomeSeq: Statistical analysis for sparse high-throughput sequencing. Bioconductor package: 1. 16.0, http://cbcb.umd.edu/software/metagenomeSeq (last access: 23 March 2017), 2016.
Pedersen, M. W., Ginolhac, A., Orlando, L., Olsen, J., Andersen, K., Holm, J., Funder, S., Willerslev, E., and Kjær, K. H.: A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa, Quaternary Sci. Rev., 75, 161–168, https://doi.org/10.1016/j.quascirev.2013.06.006, 2013.
Pedersen, M. W., Overballe-Petersen, S., Ermini, L., Sarkissian, C. Der, Haile, J., Hellstrom, M., Spens, J., Thomsen, P. F., Bohmann, K., Cappellini, E., Schnell, I. B., Wales, N. A., Caroe, C., Campos, P. F., Schmidt, A. M. Z., Gilbert, M. T. P., Hansen, A. J., Orlando, L., and Willerslev, E.: Ancient and modern environmental DNA, Philos. T. R. Soc. B, 370, 20130383–20130383, https://doi.org/10.1098/rstb.2013.0383, 2015.
R Development Core Team: R: A language and environment for statistical computing. R Foundation for Statistical Computing, http://www.r-project.org/ (last access: 23 March 2017), 2014.
Rutherford, S., D'Hondt, S., and Prell, W.: Environmental controls on the geographic distribution of zooplankton diversity, Nature, 400, 749–753, https://doi.org/10.1038/23449, 1999.
Taberlet, P., Prud'Homme, S. M., Campione, E., Roy, J., Miquel, C., Shehzad, W., Gielly, L., Rioux, D., Choler, P., Clément, J.-C., Melodelima, C., Pompanon, F., and Coissac, E.: Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies, Mol. Ecol., 21, 1816–1820, https://doi.org/10.1111/j.1365-294X.2011.05317.x, 2012.
Torti, A., Lever, M. A., and Jørgensen, B. B.: Origin, dynamics, and implications of extracellular DNA pools in marine sediments, Mar. Genomics, 24, 185–196, https://doi.org/10.1016/j.margen.2015.08.007, 2015.
Weber, A. A. T. and Pawlowski, J.: Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera, PLoS One, 8, 1–8, https://doi.org/10.1371/journal.pone.0056739, 2013.
Yasuhara, M., Tittensor, D. P., Hillebrand, H., and Worm, B.: Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model, Biol. Rev., 92, 199–215, https://doi.org/10.1111/brv.12223, 2015.
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.
The exploitation of deep-sea sedimentary archive relies on the recovery of mineralized skeletons...
Altmetrics
Final-revised paper
Preprint