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
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Andreia Rebotim, Antje Helga Luise Voelker, Lukas Jonkers, Joanna J. Waniek, Michael Schulz, and Michal Kucera
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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...
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