publications

patent

1. patent

   Système et procédé de tri particulaire, et installation et procédé de tri et de caractérisation particulaire associés

   Ross Marchant, Thibault de Garidel-Thoron, Jean-Marc Brutti, and Philippe Eloi

   Nov 2022

   Abs HTML

   Système de tri particulaire (2) pour trier et isoler des particules d’un échantillon solide particulaire contenant des particules à l’état solide, comprenant : - un contenant de séparation (4) présentant une cavité qui est en creux et délimitée par une face de fond et une face intérieure périphérique, ou une rampe (44) de forme hélicoïdale est ménagée dans la face intérieure périphérique en montant depuis la face de fond jusqu’à une extrémité supérieure débouchant hors de la cavité ; et- un dispositif vibratoire primaire (400) accouplé au contenant de séparation pour transmettre une vibration au dit contenant de mais non limitativement, pour le tri, et le cas échéant séparation. L’invention s’applique plus particulièrement, à la caractérisation, de particules ayant une taille comprise entre environ 50 micromètres et 2 millimètres, telles que des microfossiles, comme par exemple des foraminifères, des radiolaires, des ostracodes. Figure de l’abrégé : Figure 3

working papers

1. in rev

   Ecological patterns of modern planktonic foraminifera in the Bay of Bengal

   Rose Manceau, Meryem Mojtahid, Eelco Rohling, Robin Fentimen, Thibault de Garidel-Thoron, Sonia Chaabane, and Gianluca Marino

   Apr 2025

   Abs HTML

2. in rev

   Automated recognition of meso-cenozoic foraminifera from Senegalese sedimentary deposits using convolutional neural network

   Malick Thiam, Sonia Chaabane, and Thibault de Garidel-Thoron

   May 2025

   Abs HTML

3. in rev

   Contrasted trends in phytoplankton diversity, size structure and carbon burial efficiency in the NW Mediterranean Sea under shifting environmental conditions

   Camille Godbillot, Baptiste Pesenti, Karine Leblanc, Luc Beaufort, Cristèle Chevalier, Julien DiPane, Xavier Madron, Thibault de Garidel-Thoron, Thomas B. Chalk, Ralf Schiebel, Julie Meilland, and Olivier Sulpis

   Feb 2025

   Abs HTML

   Shifts in the phytoplankton assemblage induced by environmental changes have significant implications for carbon cycling and marine food webs, but remain poorly constrained across spatiotemporal scales. Here, we investigate the effects of rising sea surface temperatures and increased stratification on the phytoplankton composition and size in Northwestern Mediterranean Sea (2010-2019) using two sediment trap series: one in the oligotrophic Ligurian Sea and the other in the deep convection zone of the Gulf of Lion. We apply deep-learning image analysis to quantify phytoplankton particle fluxes, size distributions, and relative assemblages, focusing on coccolithophores, diatoms, and silicoflagellates. Our results show a general decline of phytoplankton fluxes to the seafloor, mirroring the decrease in vertical mixing in the water column. Both sites show a shift towards phytoplankton species adapted to stratified and nutrient-depleted conditions, although with contrasting patterns. In the Ligurian Sea, deep-dwelling coccolithophore species become dominant, while in the Gulf of Lion, summer-associated siliceous species, including large diatoms and silicoflagellates, show an increase. These contrasted trends, which likely result from differences in nutrient inputs and pH changes in the surface between the two sites, have implications for the efficiency of carbon export pathways at depth. Specifically, the increasing dominance of smaller phytoplankton in the Ligurian Sea leads to a reduction in carbon burial efficiency, while in the Gulf of Lion, the enhanced contribution of larger diatoms may sustain relatively higher export and burial rates in the future.

4. in rev

   Reassessment of the global distribution and diversity of modern planktonic Foraminifera from the FORCIS database

   Sonia Chaabane, Ralf Schiebel, Julie Meilland, Geert-Jan Brummer, P Graham Mortyn, Olivier Sulpis, Thomas Chalk, Xavier Giraud, Hélène Howa, Azumi Kuroyanagi, Grégory Beaugrand, and Thibault de Garidel-Thoron

   Feb 2025

   Abs HTML

   Shifts in the phytoplankton assemblage induced by environmental changes have significant implications for carbon cycling and marine food webs, but remain poorly constrained across spatiotemporal scales. Here, we investigate the effects of rising sea surface temperatures and increased stratification on the phytoplankton composition and size in Northwestern Mediterranean Sea (2010-2019) using two sediment trap series: one in the oligotrophic Ligurian Sea and the other in the deep convection zone of the Gulf of Lion. We apply deep-learning image analysis to quantify phytoplankton particle fluxes, size distributions, and relative assemblages, focusing on coccolithophores, diatoms, and silicoflagellates. Our results show a general decline of phytoplankton fluxes to the seafloor, mirroring the decrease in vertical mixing in the water column. Both sites show a shift towards phytoplankton species adapted to stratified and nutrient-depleted conditions, although with contrasting patterns. In the Ligurian Sea, deep-dwelling coccolithophore species become dominant, while in the Gulf of Lion, summer-associated siliceous species, including large diatoms and silicoflagellates, show an increase. These contrasted trends, which likely result from differences in nutrient inputs and pH changes in the surface between the two sites, have implications for the efficiency of carbon export pathways at depth. Specifically, the increasing dominance of smaller phytoplankton in the Ligurian Sea leads to a reduction in carbon burial efficiency, while in the Gulf of Lion, the enhanced contribution of larger diatoms may sustain relatively higher export and burial rates in the future.

5. in rev

   Niche contractions drive future planktonic foraminifera population and diversity loss

   Annabelle Gao, Sonia Chaabane, Gregory Beaugrand, Thibault de Garidel-Thoron, Thomas B. Chalk, Ralf Schiebel, Julie Meilland, and Olivier Sulpis

   Jan 2025

   Abs HTML

journal articles

1. P&P

   A comparison of new and established foraminiferal dissolution proxies in tropical Indian Ocean deep-sea sediments

   Michael B. Adebayo, Clara T. Bolton, Franck Bassinot, and Thibault de Garidel-Thoron

   Paleoceanography and Paleoclimatology, May 2025

   Abs HTML

   Assessing the preservation state of calcium carbonate microfossils preserved in deep-sea sediments allows us to understand the impact of ocean chemistry on deep-sea carbonate distribution and provides key information on potential biases affecting microfossil-based proxies applied in the geological past. Established dissolution indices potentially fail to capture some finer details of how dissolution affects foraminiferal assemblages, especially in intermediate depths above the lysocline. Here, we present a new dissolution index, the Fragment Variance Index (FVIndex), which estimates test preservation using the ratio between fragment size variance and whole planktonic foraminiferal test variance. We hypothesize that increasing fragment size variance will reflect better preservation, whereas increasing whole test variance will indicate dissolution linked to water depth or chemistry. We test the FVIndex and other dissolution indices on a set of 62 core-top sediment samples from the tropical Indian Ocean (TIO) using an automated imaging system (MiSo) and the ParticleTrieur software, analyzing over 220,000 foraminifera and fragments. Generally, a higher FVIndex is associated with better preservation (at shallower water depths) and vice versa. The FVIndex, supported by other indices, indicates strong dissolution impact on planktonic foraminifera assemblages in the Mozambique Channel, but very weak impact in the TIO due to the significant influence of local processes. We have tested FVIndex as a dissolution index on datasets from the Mozambique Channel and TIO; the next step would be to examine its performance in other more oceanographically homogenous regions.

2. in press

   Planktonic foraminifera test size controlled by living and post-mortem conditions

   Jaime Y. Suárez-Ibarra, Ingrid M. Vieira, Cristiane F. Frozza, Sonia Chaabane, Pamela Palhano, Vojtech Kovar, Thomas B. Chalk, Geise Anjos-Zerfass, Thibault de Garidel-Thoron, Katarina Holcova, and María A. G. Pivel

   Journal of Foraminiferal Research, Jul 2025

   Abs HTML

3. Nature

   Modern planktonic Foraminifera: migrating is not enough

   Sonia Chaabane, Thibault de Garidel-Thoron, Julie Meilland, Olivier Sulpis, Thomas Chalk, Geert-Jan Brummer, P Graham Mortyn, Xavier Giraud, Hélène Howa, Nicolas Casajus, Azumi Kuroyanagi, Grégory Beaugrand, and Ralf Schiebel

   Nature, Nov 2024

   Abs HTML

   Rising carbon dioxide emissions are provoking ocean warming and acidification1,2, altering plankton habitats and threatening calcifying organisms3, such as the planktonic foraminifera (PF). Whether the PF can cope with these unprecedented rates of environmental change, through lateral migrations and vertical displacements, is unresolved. Here we show, using data collected over the course of a century as FORCIS4 global census counts, that the PF are displaying evident poleward migratory behaviours, increasing their diversity at mid- to high latitudes and, for some species, descending in the water column. Overall foraminiferal abundances have decreased by 24.2 ± 0.1% over the past eight decades. Beyond lateral migrations5, our study has uncovered intricate vertical migration patterns among foraminiferal species, presenting a nuanced understanding of their adaptive strategies. In the temperature and calcite saturation states projected for 2050 and 2100, low-latitude foraminiferal species will face physicochemical environments that surpass their current ecological tolerances. These species may replace higher-latitude species through poleward shifts, which would reduce low-latitude foraminiferal diversity. Our insights into the adaptation of foraminifera during the Anthropocene suggest that migration will not be enough to ensure survival. This underscores the urgent need for us to understand how the interplay of climate change, ocean acidification and other stressors will impact the survivability of large parts of the marine realm.

4. JGR-Biog

   A new method for the detection of siliceous microfossils on sediment microscope slides using convolutional neural networks

   C Godbillot, R Marchant, L Beaufort, K Leblanc, Y Gally, T.D.Q. Le, C Chevalier, and T de Garidel-Thoron

   Journal of Geophysical Research: Biogeosciences, Sep 2024

   Abs HTML

   Diatom communities preserved in sediment samples are valuable indicators for understanding the past and present dynamics of phytoplankton communities, and their response to environmental changes. These studies are traditionally achieved by counting methods using optical microscopy, a time-consuming process that requires taxonomic expertise. With the advent of automated image acquisition workflows, large image datasets can now be acquired, but raise the need for efficient preprocessing methods. Detecting diatom frustules on microscope images is a challenge due to their low relief, diverse shapes, and tendency to aggregate, which prevent the use of traditional thresholding techniques. Deep learning algorithms have the potential to resolve these challenges, more particularly for the task of object detection. Here we explore the use of a Faster R-CNN (Region-based Convolutional Neural Network) model to detect siliceous biominerals, including diatoms, in microscope images of a sediment trap series from the Mediterranean Sea. Our workflow demonstrates promising results, achieving a precision score of 0.72 and a recall score of 0.74 when applied to a test set of Mediterranean diatom images. Our model performance decreases when used to detect fragments of these microfossils; it also decreases when particles are aggregated or when images are out of focus. Microfossil detection remains high when the model is used on a microscope image set of sediments from a different oceanic basin, demonstrating its potential for application in a wide range of contemporary and paleoenvironmental studies. This automated method provides a valuable tool for analyzing complex samples, particularly for rare species under-represented in training datasets.

5. L&O Meth

   Size harmonizing planktonic Foraminifera number concentrations in the water column

   Sonia Chaabane, Thibault de Garidel-Thoron, Xavier Giraud, Julie Meilland, Geert-Jan Brummer, Lukas Jonkers, Mattia Greco, Graham Mortyn, Nicolas Casajus, Michal Kucera, Azumi Kuroyanagi, Hélène Howa, Fanny Monteiro, Gregory Beaugrand, and Ralf Schiebel

   Limnology and Oceanography-Methods, Jul 2024

   Abs HTML

   Planktonic Foraminifera have been collected from the water column with different plankton sampling devices equipped with nets of various mesh sizes, which impedes direct comparison of observed quantifications. Here, we use data on the community size structure of planktonic Foraminifera to assess the impact of mesh size on the measured abundance (ind m−3) of planktonic Foraminifera. We use data from the FORCIS database (Chaabane et al., 2023, Scientific Data 10: 354) on the global ocean at different sampling depths over the past century. We find a global cumulative increase in abundance with size, which is best described using a Michaelis–Menten function. This function yields multiplication factors by which one size fraction can be normalized to any other size fraction equal to or larger than 100 μm. The resulting size normalization model is calibrated over a range of different depth intervals, and validated with an independent dataset from various depth ranges. The comparison to Berger’s (1969, Deep. Res. Oceanogr. Abstr. 16: 1–24) equivalent catch approach shows a significant increase in the predictive skill of the model. The new size normalization scheme enables comparison of Foraminifera abundance data sampled with plankton nets of different mesh sizes, such as compiled in the FORCIS database. The correction methodology may be effectively employed for various other plankton groups such as diatoms and dinoflagellates.

6. new phyt

   Guidelines for getting accurate automated pollen counts using YOLOv5 on real-world samples collected in the Mediterranean region

   B Gimenez, S Joannin, J Pasquet, L Beaufort, Y Gally, T de Garidel-Thoron, N Combourieu-Nebout, L Bouby, S Canal, S Ivorra, B Limier, J F Terral, C Devaux, and O Peyron

   Methods in Ecology and Evolution, May 2024

   Abs HTML

   Reconstructing current and past vegetation with pollen still relies on tedious manual detection and identification. Most recent works on automated pollen analyses have focused on classification, while the first step - detection - remains overlooked, although critical as detection errors will propagate to classification. Detection can be complex when applied on real-world samples containing many debriWs and pollen taxa, and pollen that can be damaged or clumped. Here, we used the popular algorithm YOLOv5 to evaluate its detection performance on pollen slides mounted directly from annual passive traps. We aim to provide comprehensive implementation guidelines: share insights on how to optimize its use for pollen studies, and how to annotate pollen to trade-off labour work and performance. We acquired with an automated microscope 1,024 images for each of 16 samples collected three consecutive years in six locations in Southern France. We trained YOLOv5 to detect pollen grains on 4,098 images containing 12,531 manually tagged and labeled grains, while testing for several strategies to build the training dataset and annotate the images. We evaluated the performance under each strategy, and analyzed the causes of the detection errors. We finally tested the most detailed annotation strategy for pollen classification on 5 taxa, and validated it with manual identification. Only 5.2% of pollen grains and Lycopodium spores (used to calibrate pollen counts) were left undetected, and 5.3% of debris were falsely detected as pollen. Undetected pollen grains had rare morphologies, were covered by debris, unfocused in the images, or cut in the images. Labeling pollen with their taxa did not improve detection, and, tagging and labeling one specific taxon decreased the annotation workload but was accurate only for morphologically specific taxa. Applying the trained YOLOv5 on images from new pollen correlated well with counts made by a palynologist. Our results complement pioneer studies on automated pollen analyses from real-world samples, as they provide common causes for detection errors, and guidelines to optimize detection. Automating pollen detection will increase the spatial and temporal resolutions of pollen studies.

7. BioRev

   The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in the plankton

   Raphael Morard, Kate F Darling, Tristan Cordier, Nicolas Henry, Christiane Hassenruck, Chiara Vanni, Mattia Greco, Agnes K M Weiner, Nele Vollmar, Tamara Milivojevic, Nurshan Rahman, Michael Siccha, Julie Meilland, Lukas Jonkers, Frédéric Quillévéré, Gilles Escarguel, Christophe J Douady, Thibault de Garidel-Thoron, Colomban Vargas, and Michal Kucera

   Biological Reviews, Feb 2024

   Abs

   ABSTRACT The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of  7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering  1700 samples with  2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across  1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence.

8. Front

   Surface fertilisation and organic matter delivery enhanced carbonate dissolution in the western South Atlantic

   Jaime Y. Suárez-Ibarra, Tiago M. Freire, Cristiane F. Frozza, Tainã M. L. Pinho, Sandro M. Petró, Bruna B. Dias, Thomas B. Chalk, Sonia Chaabane, Medhavi Srivastava, Karen B. Costa, Felipe A. L. Toledo, Thibault de Garidel-Thoron, João C. Coimbra, and María A. G. Pivel

   Frontiers in Ecology and Evolution, Feb 2023

   Abs HTML

   The last glacial inception was characterised by rapid changes in temperature, atmospheric pCO₂, and changes in the water mass geometry of the major ocean basins. Although several climatic feedback mechanisms have been proposed to explain the glacial/interglacial cycles witnessed in the Quaternary, the exact mechanistic responses of these processes are still under constrained. In this study we use proxies including planktonic foraminifera compositional assemblages and oxygen stable isotopes to reconstruct past changes in sea surface productivity, stratification, and carbonate dissolution. We use core SIS-249 (2,091 mbsl, western South Atlantic 30°S 47°W), spanning 30–110 thousand years ago (ka), and currently bathed by modern Northern Component Water. We test existing hypotheses suggesting that the orbital obliquity cycle modulates the biological pump in the study area. Spectral analysis run on our synthesised productivity proxies recognises a  43 kyr-cycle, related to the obliquity cycle. We propose that the enhanced productivity is produced by two mechanisms: i) the glacial upwelling of subsurface nutrient-rich waters and, ii) the continental (wind-driven dust and riverine outflows) fertilisation of the photic zone, with the latter process being obliquity-paced. We also suggest that not only the increased organic matter export but also a change in its bioavailability (from refractory to labile) led to calcium carbonate dissolution, as the degradation of the more soluble organic matter decreased the pH of the glacial bottom water, partially dissolving the calcium carbonate. Although our correlation analyses show a strong benthic-pelagic coupling through the relation between the enhanced biological pump and carbonate dissolution (ρ<0.05, r=0.80), we cannot reject the potential of corrosive Southern Component Water bathing the site during the glacial. Finally, we highlight that these processes are not mutually exclusive and that both can be modulated by the obliquity cycle.

9. GPC

   Glacial expansion of carbon-rich deep waters into the Southwestern Indian Ocean over the last 630 kyr

   José N Pérez-Asensio, Kazuyo Tachikawa, Laurence Vidal, Thibault de Garidel-Thoron, Corinne Sonzogni, Abel Guihou, Pierre Deschamps, Stéphan J Jorry, and Min-Te Chen

   Glob. Planet. Change, Oct 2023

   Abs HTML

   Oceanic carbon storage is one of the main sinks for atmospheric CO2, and thought to be the major contributing factor for CO2 drawdown during past glacial periods. Both physical and biogeochemical processes control the capacity of carbon storage in the ocean. During glacial periods of the Pleistocene the larger volume of deep-water masses of Southern Hemisphere origin in the Atlantic has been shown to promote carbon storage in the Southern Ocean. However, the latitudinal extension of this water mass in the Indian Ocean has been scarcely studied. In this study, we combine foraminiferal \epsilonNd and benthic \delta13C of two sediment cores in the southwest Indian Ocean (MD96–2077, 33°S, 3781 m water depth; MD96–2052, 19°S, 2627 m water depth), to reconstruct the spatial and temporal evolution of glacial carbon-rich deep waters in the SW Indian over the last 630 kyr. The combined use of foraminiferal \epsilonNd and benthic \delta13C allows to distinguish \delta13C changes related to water mass mixing and from respired carbon accumulation within the water masses. Nutrient-rich deep waters, which cannot be explained by the enhanced proportion of southern-sourced waters, were present at core sites deeper than 2700 m during glacial periods and extended at least until 33°S into the SW Indian Ocean. From Marine Isotope Stage (MIS) 14 to MIS 10, glacial carbon storage increased gradually until reaching its highest capacity during the extreme glacial periods MIS 12 and 10. Orbital forcing (100-kyr eccentricity, 41-kyr obliquity), restricted air-sea exchange and enhanced ocean stratification, fostered higher carbon storage during periods of relatively lower eccentricity and obliquity. Furthermore, after MIS 10, a progressive transition was observed from 100-kyr eccentricity to 41-kyr obliquity cycles in benthic \delta13C and \delta18O records of core MD96–2077 and sea-ice cover changes derived from ice-rafted debris of the Agulhas Plateau composite core site.

10. SciData

    The FORCIS database: A global census of planktonic Foraminifera from ocean waters

    Sonia Chaabane, Thibault de Garidel-Thoron, Xavier Giraud, Ralf Schiebel, Gregory Beaugrand, Geert-Jan Brummer, Nicolas Casajus, Mattia Greco, Maria Grigoratou, Helene Howa, Lukas Jonkers, Michal Kucera, Azumi Kuroyanagi, Julie Meilland, Fanny Monteiro, Graham Mortyn, Ahuva Almogi-Labin, Hirofumi Asahi, Simona Avnaim-Katav, Franck Bassinot, Catherine V. Davis, David B. Field, Ivan Hernandez-Almeida, Barak Herut, Graham Hosie, Will Howard, Anna Jentzen, David G. Johns, Lloyd Keigwin, John Kitchener, Karen E. Kohfeld, Douglas V. O. Lessa, Clara Manno, Margarita Marchant, Siri Ofstad, Joseph D. Ortiz, Alexandra Post, Andres Rigual-Hernandez, Marina C. Rillo, Karen Robinson, Takuya Sagawa, Francisco Sierro, Kunio T. Takahashi, Adi Torfstein, Igor Venancio, Makoto Yamasaki, and Patrizia Ziveri

    Scientific Data, Jun 2023

    Abs HTML

    Planktonic Foraminifera (PF) are unicellular eukaryotes that play a key role in the marine carbon cycle and are important indicators of past ocean conditions. The FORCIS database is a global census of planktonic Foraminifera from ocean waters, providing a comprehensive resource for researchers studying these organisms. The database includes data on species composition, abundance, and size distribution from over 1,000 samples collected from various oceanic regions. The FORCIS database is freely accessible and can be used to investigate the distribution and diversity of planktonic Foraminifera in relation to environmental factors such as temperature, salinity, and nutrient availability. This resource will facilitate further research on the ecological and biogeochemical roles of planktonic Foraminifera in the world’s oceans.

11. G-cubed

    Environmental Controls of Size Distribution of Modern Planktonic Foraminifera in the Tropical Indian Ocean

    Michael B. Adebayo, Clara T. Bolton, Ross Marchant, Franck Bassinot, Sandrine Conrod, and Thibault de Garidel-Thoron

    Geochemistry Geophysics Geosystems, Apr 2023

    Abs HTML

    Paleoceanographic studies often rely on abundance changes in microfossil species, with little consideration for characteristics such as organism size, which may also be related to environmental changes. Using a tropical Indian Ocean (TIO) core-top data set, we test the Optimum size-hypothesis (OSH), investigating whether relative abundance or environmental variables are better descriptors of planktonic foraminifera species’ optimum conditions. We also investigate the environmental drivers of whole-assemblage planktonic foraminiferal test size variation in the TIO. We use an automated imaging and sorting system (MiSo) to identify planktonic foraminiferal species, analyze their morphology, and quantify fragmentation rate using machine learning techniques. Machine model accuracy is confirmed by comparison with human classifiers (97% accuracy). Data for 33 environmental parameters were extracted from modern databases and, through exploratory factor analysis and regression models, we explore relationships between planktonic foraminiferal size and oceanographic parameters in the TIO. Results show that the size frequency distribution of most planktonic foraminifera species is unimodal, with some larger species showing multimodal distributions. Assemblage size95/5 (95th percentile size) increases with increasing species diversity, and this is attributed to vertical niche separation induced by thermal stratification. Our test for the OSH reveals that relative abundance is not a good predictor of species’ optima and within-species size95/5 response to environmental parameters is species-specific, with parameters related to carbonate ion concentration, temperature, and salinity being primary drivers. At the species and assemblage levels, our analyses indicate that carbonate ion concentration and temperature play important roles in determining size trends in TIO planktonic foraminifera.

12. MPB

    Contamination of planktonic food webs in the Mediterranean Sea: Setting the frame for the MERITE-HIPPOCAMPE oceanographic cruise (spring 2019)

    Marc Tedetti, Jacek Tronczynski, Francois Carlotti, Marc Pagano, Sana Ben Ismail, Cherif Sammari, Malika Bel Hassen, Karine Desboeufs, Charlotte Poindron, Sandrine Chifflet, Amel Bellaaj Zouari, Moufida Abdennadher, Sirine Amri, Daniela Banaru, Lotfi Ben Abdallah, Nagib Bhairy, Ismail Boudriga, Aude Bourin, Christophe Brach-Papa, Nicolas Briant, Lea Cabrol, Cristele Chevalier, Lassaad Chouba, Sylvain Coudray, Mohamed Nejib Daly Yahia, Thibault de Garidel-Thoron, Aurelie Dufour, Jean-Claude Dutay, Boris Espinasse, Pamela Fierro-Gonzalez, Michel Fornier, Nicole Garcia, Franck Giner, Catherine Guigue, Loic Guilloux, Asma Hamza, Lars-Eric Heimbuerger-Boavida, Stephanic Jacquet, Joel Knoery, Rim Lajnef, Nouha Makhlouf Belkahia, Deny Malengros, Pauline L. Martinot, Anthony Bosse, Jean-Charles Mazur, Marouan Meddeb, Benjamin Misson, Olivier Pringault, Marianne Quemeneur, Olivier Radakovitch, Patrick Raimbault, Christophe Ravel, Vincent Rossi, Chaimaa Rwawi, Asma Sakka Hlaili, Javier Angel Tesan-Onrubia, Bastien Thomas, Melilotus Thyssen, Noureddine Zaaboub, and Cedric Garnier

    Marine Pollution Bulletin, Apr 2023

    Abs HTML

    This paper looks at experiential feedback and the technical and scientific challenges tied to the MERITE-HIPPOCAMPE cruise that took place in the Mediterranean Sea in spring 2019. This cruise proposes an innovative approach to investigate the accumulation and transfer of inorganic and organic contaminants within the planktonic food webs. We present detailed information on how the cruise worked, including 1) the cruise track and sampling stations, 2) the overall strategy, based mainly on the collection of plankton, suspended particles and water at the deep chlorophyll maximum, and the separation of these particles and planktonic organisms into various size fractions, as well as the collection of atmospheric deposition, 3) the operations performed and material used at each station, and 4) the sequence of operations and main parameters analysed. The paper also provides the main environmental conditions that were prevailing during the campaign. Lastly, we present the types of articles produced based on work completed by the cruise that are part of this special issue.

13. L&O

    Machine learning techniques to characterize functional traits of plankton from image data

    Eric C. Orenstein, Sakina-Dorothee Ayata, Frederic Maps, Erica C. Becker, Fabio Benedetti, Tristan Biard, Thibault de Garidel-Thoron, Jeffrey S. Ellen, Filippo Ferrario, Sarah L. C. Giering, Tamar Guy-Haim, Laura Hoebeke, Morten Hvitfeldt Iversen, Thomas Kiorboe, Jean-Francois Lalonde, Arancha Lana, Martin Laviale, Fabien Lombard, Tom Lorimer, Severine Martini, Albin Meyer, Klas Ove Moeller, Barbara Niehoff, Mark D. Ohman, Cedric Pradalier, Jean-Baptiste Romagnan, Simon-Martin Schroeder, Virginie Sonnet, Heidi M. Sosik, Lars S. Stemmann, Michiel Stock, Tuba Terbiyik-Kurt, Nerea Valcarcel-Perez, Laure Vilgrain, Guillaume Wacquet, Anya M. Waite, and Jean-Olivier Irisson

    Limnology and Oceanography, Aug 2022

    Abs HTML

    Plankton imaging systems supported by automated classification and analysis have improved ecologists’ ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.

14. Front

    The Foraminiferal Response to Climate Stressors Project: Tracking the Community Response of Planktonic Foraminifera to Historical Climate Change

    Thibault de Garidel-Thoron, Sonia Chaabane, Xavier Giraud, Julie Meilland, Lukas Jonkers, Michal Kucera, Geert-Jan A. Brummer, Maria Grigoratou, Fanny M. Monteiro, Mattia Greco, P. Graham Mortyn, Azumi Kuroyanagi, Helene Howa, Gregory Beaugrand, and Ralf Schiebel

    Frontiers in Marine Science, May 2022

    Abs HTML

    Planktonic Foraminifera are ubiquitous marine protozoa inhabiting the upper ocean. During life, they secrete calcareous shells, which accumulate in marine sediments, providing a geological record of past spatial and temporal changes in their community structure. As a result, they provide the opportunity to analyze both current and historical patterns of species distribution and community turnover in this plankton group on a global scale. The FORCIS project aims to unlock this potential by synthesizing a comprehensive global database of abundance and diversity observations of living planktonic Foraminifera in the upper ocean over more than 100 years starting from 1910. The database will allow for unravelling the impact of multiple global-change stressors acting on planktonic Foraminifera in historical times, using an approach that combines statistical analysis of temporal diversity changes in response to environmental changes with numerical modeling of species response based on their ecological traits.

15. ICESjms

    Linking zooplankton time series to the fossil record

    Lukas Jonkers, Julie Meilland, Marina C. Rillo, Thibault de Garidel-Thoron, John A. Kitchener, and Michal Kucera

    ICES Journal of Marine Science, Apr 2022

    Abs HTML

    Marine zooplankton time series are crucial to understand the dynamics of pelagic ecosystems. However, most observational time series are only a few decades long, which limits our understanding of long-term zooplankton dynamics, renders attribution of observed trends to global change ambiguous, and hampers prediction of future response to environmental change. Planktonic foraminifera are calcifying marine zooplankton that have the unique potential to substantially extend our view on plankton dynamics because their skeletal remains are preserved for millions of years in deep-sea sediments. Thus, linking sedimentary and modern time series offers great potential to study zooplankton dynamics across time scales not accessible by direct observations. However, this link is rarely made and the potential of planktonic foraminifera for advancing our understanding of zooplankton dynamics remains underexploited. This underutilization of this potential to bridge time scales is mainly because of the lack of collaboration between biologists, who have mostly focused on other (zoo)plankton, and micropalaeontologists, who have focussed too narrowly on fossil foraminifera. With this food for thought article, we aim to highlight the unique potential of planktonic foraminifera to bridge the gap between biology and geology. We strongly believe that such collaboration has large benefits to both scientific communities.

16. CP

    Technical note: A new automated radiolarian image acquisition, stacking, processing, segmentation and identification workflow

    Martin Tetard, Ross Marchant, Giuseppe Cortese, Yves Gally, Thibault de Garidel-Thoron, and Luc Beaufort

    Climate of the Past, Dec 2020

    Abs HTML

    Identification of microfossils is usually done by expert taxonomists and requires time and a significant amount of systematic knowledge developed over many years. These studies require manual identification of numerous specimens in many samples under a microscope, which is very tedious and time-consuming. Furthermore, identification may differ between operators, biasing reproducibility. Recent technological advances in image acquisition, processing and recognition now enable automated procedures for this process, from microscope image acquisition to taxonomic identification. A new workflow has been developed for automated radiolarian image acquisition, stacking, processing, segmentation and identification. The protocol includes a newly proposed methodology for preparing radiolarian microscopic slides. We mount eight samples per slide, using a recently developed 3D-printed decanter that enables the random and uniform settling of particles and minimizes the loss of material. Once ready, slides are automatically imaged using a transmitted light microscope. About 4000 specimens per slide (500 per sample) are captured in digital images that include stacking techniques to improve their focus and sharpness. Automated image processing and segmentation is then performed using a custom plug-in developed for the ImageJ software. Each individual radiolarian image is automatically classified by a convolutional neural network (CNN) trained on a Neogene to Quaternary radiolarian database (currently 21 746 images, corresponding to 132 classes) using the ParticleTrieur software. The trained CNN has an overall accuracy of about 90%. The whole procedure, including the image acquisition, stacking, processing, segmentation and recognition, is entirely automated via a LabVIEW interface, and it takes approximately 1 h per sample. Census data count and classified radiolarian images are then automatically exported and saved. This new workflow paves the way for the analysis of long-term, radiolarian-based palaeoclimatic records from siliceous-remnant-bearing samples.

17. MarGeol

    Magnetic fabric of Bengal fan sediments: Holocene record of sedimentary processes and turbidite activity from the Ganges-Brahmaputra river system

    Eva Moreno, Fabien Caroir, Lea Fournier, Kelly Fauquembergue, Sebastien Zaragosi, Ronan Joussain, Christophe Colin, Marie-Madeleine Blanc-Valleron, Francois Baudin, Thibault de Garidel-Thoron, Jean Pierre Valet, and Franck Bassinot

    Marine Geology, Dec 2020

    Abs HTML

    We present here a study based on the Anisotropy of Magnetic Susceptibility (AMS) and magnetic mineralogy carried out on the composite core MD17&18taken from the eastern levee of the active channel of the middle Bengal Fan in the Indian Ocean. Based on C-14 dating, the sedimentary sequence covers 9.8 ka in 39 m of sediment. It therefore records at very high resolution the variations in continental material exported to the ocean by the Ganges-Brahmaputra river system during the Holocene. This sequence was divided into two units according to turbidite activity: Unit 1 from 9.8 to 9.2 ka cal. BP representing 39 m of coarse-grained turbidite sequences (coarse silts to fine sands) and extremely high sedimentation rates. Unit 2 of 9.2 ka cal. BP to the present characterized by a sharp decrease in the sedimentation rate, the presence of fine-grained turbidites characterized by strong decrease in the ln(Ti/Ca) ratio. Our AMS results indicate that the magnetic fabric is highly sensitive to the mode of deposition. The turbidite sequences are clearly characterized by very high F and Pj values, not only of the coarse-grained turbidite levels in unit 1, but also of the fine turbidites in unit 2. We suggest that this strong degree of anisotropy is the result of the strong and rapid deposition during the turbidite sequences which induces an additional compaction effect. Furthermore, low temperature SIRM measurements revealed that the magnetic minerals representative of the Ganges and Brahmaputra drainage area are magnetite, hematite and goethite. A higher supply in fine-grained magnetite was observed during the turbidite sequences in phase with an increase in sediment grain size.

18. JoMP

    Automated analysis of foraminifera fossil records by image classification using a convolutional neural network

    Ross Marchant, Martin Tetard, Adnya Pratiwi, Michael Adebayo, and Thibault de Garidel-Thoron

    Journal of Micropaleontology, Oct 2020

    Abs HTML

    Manual identification of foraminiferal morphospecies or morphotypes under stereo microscopes is time consuming for micropalaeontologists and not possible for nonspecialists. Therefore, a long-term goal has been to automate this process to improve its efficiency and repeatability. Recent advances in computation hardware have seen deep convolutional neural networks emerge as the state-of-the-art technique for image-based automated classification. Here, we describe a method for classifying large foraminifera image sets using convolutional neural networks. Construction of the classifier is demonstrated on the publicly available Endless Forams image set with a best accuracy of approximately 90 %. A complete automatic analysis is performed for benthic species dated to the last deglacial period for a sediment core from the north-eastern Pacific and for planktonic species dated from the present until 180 000 years ago in a core from the western Pacific warm pool. The relative abundances from automatic counting based on more than 500 000 images compare favourably with manual counting, showing the same signal dynamics. Our workflow opens the way to automated palaeoceanographic reconstruction based on computer image analysis and is freely available for use.

19. SciRep

    Nanoscale trace metal imprinting of biocalcification of planktic foraminifers by Toba’s super-eruption

    L. Lemelle, A. Bartolini, A. Simionovici, R. Tucoulou, W. De Nolf, F. Bassinot, and T. de Garidel-Thoron

    Scientific Reports, Jul 2020

    Abs HTML

    Bioactive metal releases in ocean surface water, such as those by ash falls during volcanic super-eruptions, might have a potentially toxic impact on biocalcifier planktic microorganisms. Nano-XRF imaging with the cutting-edge synchrotron hard X-ray nano-analysis ID16B beamline (ESRF) revealed for the first time a specific Zn- and Mn-rich banding pattern in the test walls of Globorotalia menardii planktic foraminifers extracted from the Young Toba Tuff layer, and thus contemporaneous with Toba’s super-eruption, 74,000 years ago. The intra-test correlation of Zn and Mn patterns at the nanoscale with the layered calcareous microarchitecture, indicates that the incorporation of these metals is syngenetic to the wall growth. The preferential Mn and Zn sequestration within the incipient stages of chamber formation suggests a selective incorporation mechanism providing a resilience strategy to metal pollution in the test building of planktic foraminifers.

20. C&G

    Automated recognition by multiple convolutional neural networks of modern, fossil, intact and damaged pollen grains

    Benjamin Bourel, Ross Marchant, Thibault de Garidel-Thoron, Martin Tetard, Doris Barboni, Yves Gally, and Luc Beaufort

    Computers & Geosciences, Jul 2020

    Abs HTML

    Pollen grains are valuable paleoclimate and paleovegetation proxies which require extensive knowledge of morphotypes and long acquisition time under the microscope. The abundance of damaged, folded, and broken pollen grains in the fossil register and sometimes also in modern soil and sediment samples, has so far prevented automation of pollen identification. Recent improvements in machine learning, however, have allowed reconsidering this approach. Here we present an automated approach which is capable of assisting palynologists with poorly preserved pollen samples. Called multi-CNNs, this approach is based on multiple convolutional neural networks (CNNs) integrated in a decision tree system. To test it, we built a system designed for three botanical families very common in the modern and fossil pollen assemblages of Eastern Africa, namely Amaranthaceae, Poaceae, and Cyperaceae. Our system was tested on stacked optical images of 8 pollen types (6 Amaranthaceae, 1 Poaceae, 1 Cyperaceae) using a training dataset of 1102 intact pollen grains and three validation datasets of intact (276 grains), damaged (223 grains), and fossil pollen (97 grains). We show that our system successfully recognizes intact, damaged, and fossil pollen grains with very low misclassification rates of 0%, 2.8%, and 3.7%, respectively. The use of augmentation on stacked optical images during the training increases classification accuracy. Following a palynologist’s approach, our system allows grains without obvious characters to be classified into a class of high taxonomic level or as indeterminable pollen. This is the first software able to process grains with a wide range of taphonomical stages, which makes it the first truly applicable to automated pollen identification of fossil material.

21. PLOS

    Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides

    Raphael Morard, Angelina Fuellberg, Geert-Jan A. Brummer, Mattia Greco, Lukas Jonkers, Andre Wizemann, Agnes K. M. Weiner, Kate Darling, Michael Siccha, Ronan Ledevin, Hiroshi Kitazato, Thibault de Garidel-Thoron, Colomban Vargas, and Michal Kucera

    PLOS One, Dec 2019

    Abs HTML

    The planktonic foraminifera genus Globigerinoides provides a prime example of a species-rich genus in which genetic and morphological divergence are uncorrelated. To shed light on the evolutionary processes that lead to the present-day diversity of Globigerinoides, we investigated the genetic, ecological and morphological divergence of its constituent species. We assembled a global collection of single-cell barcode sequences and show that the genus consists of eight distinct genetic types organized in five extant morphospecies. Based on morphological evidence, we reassign the species Globoturborotalita tenella to Globigerinoides and amend Globigerinoides ruber by formally proposing two new subspecies, G. ruber albus n.subsp. and G. ruber ruber in order to express their subspecies level distinction and to replace the informal G. ruber "white" and G. ruber "pink", respectively. The genetic types within G. ruber and Globigerinoides elongatus show a combination of endemism and coexistence, with little evidence for ecological differentiation. CT-scanning and ontogeny analysis reveal that the diagnostic differences in adult morphologies could be explained by alterations of the ontogenetic trajectories towards final (reproductive) size. This indicates that heterochrony may have caused the observed decoupling between genetic and morphological diversification within the genus. We find little evidence for environmental forcing of either the genetic or the morphological diversification, which allude to biotic interactions such as symbiosis, as the driver of speciation in Globigerinoides.

22. RevMic

    Advances in planktonic foraminifer research: New perspectives for paleoceanography

    Ralf Schiebel, Sandi M. Smart, Anna Jentzen, Lukas Jonkers, Raphael Morard, Julie Meilland, Elisabeth Michel, Helen K. Coxall, Pincelli M. Hull, Thibault de Garidel-Thoron, Tracy Aze, Frederic Quillevere, Haojia Ren, Daniel M. Sigman, Hubert B. Vonhof, Alfredo Martinez-Garcia, Michal Kucera, Jelle Bijma, Howard J. Spero, and Gerald H. Haug

    Revue de Micropaleontologie, Dec 2018

    Abs HTML

    Planktonic foraminifer tests are major archives of environmental change and provide a multitude of proxies in paleoceanography and paleoclimatology. The application of such proxies is contingent upon a collaborative effort to better understand how the living organisms record the properties of their environment and how the resulting signals are recorded in marine sediments. In this contribution, we provide a review of the rapidly developing sub-fields of research, where new advances have been made possible by technological developments, and by cross-disciplinary work of the scientific community. Following brief historical overviews of the sub-fields, we discuss the latest advances in planktonic foraminifer research and highlight the resulting new perspectives in ocean and climate research. Natural classification based on consistent species concepts forms the basis for analysis of any foraminifer-derived proxy. New approaches in taxonomy and phylogeny of Cenozoic planktonic foraminifers (Section 2) are presented, highlighting new perspectives on sensitivity and response of planktonic foraminifers to the changing climate and environment (Section 4). Calibration of foraminifer-specific data and environmental parameters is improving along with the technical development of probes and the access to samples from the natural environment (Section 3), enhancing our understanding of the ever-changing climate and ocean system. Comprehension of sedimentation and flux dynamics facilitates maximum gain of information from fossil assemblages (Section 5). Subtle changes in the physical (e.g., temperature), chemical (e.g., pH), and biological (e.g., food) conditions of ambient seawater affect the abundance of species and composition of assemblages as well as the chemical composition of the foraminifer shell and provide increasingly-detailed proxy data on paleoenvironments (Section 6).

23. Paleoc

    North Atlantic Midlatitude Surface-Circulation Changes Through the Plio-Pleistocene Intensification of Northern Hemisphere Glaciation

    Clara T. Bolton, Ian Bailey, Oliver Friedrich, Kazuyo Tachikawa, Thibault de Garidel-Thoron, Laurence Vidal, Corinne Sonzogni, Gianluca Marino, Eelco J. Rohling, Marci M. Robinson, Magali Ermini, Mirjam Koch, Matthew J. Cooper, and Paul A. Wilson

    Paleoceanography and Paleoclimatology, Nov 2018

    Abs HTML

    The North Atlantic Current (NAC) transports warm salty water to high northern latitudes, with important repercussions for ocean circulation and global climate. A southward displacement of the NAC and Subarctic Front, which separate subpolar and subtropical water masses, is widely suggested for the Last Glacial Maximum (LGM) and may have acted as a positive feedback in glacial expansion at this time. However, the role of the NAC during the intensification of Northern Hemisphere glaciation (iNHG) at  3.5 to 2.5 Ma is less clear. Here we present new records from Integrated Ocean Drilling Program Site U1313 (41°N) spanning  2.8–2.4 Ma to trace the influence of Subarctic Front waters above this mid-latitude site. We reconstruct surface and permanent pycnocline temperatures and seawater δ18O using paired Mg/Ca-δ18O measurements on the planktic foraminifers Globigerinoides ruber and Globorotalia crassaformis and determine abundances of the subpolar foraminifer Neogloboquadrina atlantica. We find that the first significant glacial incursions of Subarctic Front surface waters above Site U1313 did not occur until  2.6 Ma. At no time during our study interval was (sub)surface reorganization in the midlatitude North Atlantic analogous to the LGM. Our findings suggest that LGM-like processes sensu stricto cannot be invoked to explain interglacial-glacial cycle amplification during iNHG. They also imply that increased glacial productivity at Site U1313 during iNHG was not only driven by southward deflections of the Subarctic Front. We suggest that nutrient injection from cold-core eddies and enhanced glacial dust delivery may have played additional roles in increasing export productivity in the midlatitude North Atlantic from 2.7 Ma.

24. Quat

    Databases for sea surface paleotemperature based on geochemical proxies from marine sediments: implications for model-data comparisons

    Guillaume Leduc, Thibault de Garidel-Thoron, Jerome Kaiser, Clara Bolton, and Camille Contoux

    Quaternaire, Jun 2017

    Abs HTML

    The Paleoclimate Model Intercomparison Project (PMIP) aims to simulate the response of Earth’s climate system to changes in different climate forcing factors, focusing on six key intervals of the geological past (the mid-Piacenzian Warm Period at  3.3-3.0 Ma, the last interglacial period at  127 ka, the last glacial maximum at  21 ka, the mid-Holocene at  6 ka, the last millennium i.e. the 850-1850 Common Era (CE) time window, as well as the last glacial termination, i.e. the  21-9 ka time window). Model evaluation is ultimately achieved via model-data comparison exercises, and such diagnoses rely on databases of proxy-based paleoclimate reconstructions available in the literature. In this context, we provide a review of the main geochemical sea surface temperature (SST) proxies (namely foraminiferal Mg/Ca ratio, the UK’37, and the TEX86) that are routinely used to aliment databases used in model-data comparisons, focusing on proxy systematics and specificities that may affect or bias SSTs reconstructed with each of these proxies. We then go on to discuss notorious mismatches between SST estimates derived from different proxies for all periods studied in PMIP, and aim to provide guidance for a better interpretation of these model-data mismatches. This review is deliberately aimed at helping the paleoclimate modeling community to better appraise how information on past SST variability is transferred to the marine geological record. In particular, when SST estimates based on different proxies provide contrasting SST signals, we stress the importance of looking at those contrasting signals through the prism of the ecology of the organisms at the origin of the SST proxies.

25. sysbiol

    Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera

    Raphael Morard, Gilles Escarguel, Agnes K. M. Weiner, Aurore Andre, Christophe J. Douady, Christopher M. Wade, Kate F. Darling, Yurika Ujiie, Heidi A. Seears, Frederic Quillevere, Thibault de Garidel-Thoron, Colomban Vargas, and Michal Kucera

    Systematic Biology, Sep 2016

    Abs HTML

    Investigations of biodiversity, biogeography, and ecological processes rely on the identification of “species” as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.

26. MarEcoRes

    PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution

    Raphael Morard, Kate F. Darling, Frederic Mahe, Stephane Audic, Yurika Ujiie, Agnes K. M. Weiner, Aurore Andre, Heidi A. Seears, Christopher M. Wade, Frederic Quillevere, Christophe J. Douady, Gilles Escarguel, Thibault de Garidel-Thoron, Michael Siccha, Michal Kucera, and Colomban Vargas

    Molecular Ecology Resources, Nov 2015

    Abs HTML

    Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR2, the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR2 website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.

27. Paleoc

    Progressive shoaling of the equatorial Pacific thermocline over the last eight glacial periods

    Fabienne Regoli, Thibault de Garidel-Thoron, Kazuyo Tachikawa, Zhiming Jian, Liming Ye, Andre W. Droxler, Guillaume Lenoir, Michel Crucifix, Nicolas Barbarin, and Luc Beaufort

    Paleoceanography, May 2015

    Abs HTML

    TThe depth of equatorial Pacific thermocline is diagnostic of the main modes of tropical climates. Past estimates of Pacific thermocline dynamics have been reconstructed either for the Last Glacial Maximum or on longer timescales at low resolution. Here we document a new high-resolution set of reconstructed past sea surface and subsurface waters temperatures from the southwestern subequatorial Pacific, core MD05-2930, in the Gulf of Papua, over the last 800 ka. We used two morphotypes of Globigerinoides ruber known to live at different water depths to reconstruct past stratification. We estimated calcification temperature of each morphotypes by Mg/Ca paleothermometry. Our subequatorial Pacific thermocline paleotemperature record indicates a response of the thermocline to both direct orbital forcing and glacial-interglacial changes. Our stratification record shows a systematic shallower glacial thermocline, whereas sea surface temperatures are characterized by precessional forcing. The record is indicative of a progressive long-term shoaling of the thermocline during the glacial stages during the late Pleistocene. The shoaling of the subequatorial Pacific thermocline is consistent with regional estimates. An enhanced South Pacific shallow overturning wind-driven circulation could have driven this progressive shoaling. We speculate that this late Pleistocene glacial shoaling of the thermocline could be related to an increase in the amplitude of the obliquity.

28. Plos

    SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications

    Aurore Andre, Frederic Quillevere, Raphael Morard, Yurika Ujiie, Gilles Escarguel, Colomban Vargas, Thibault de Garidel-Thoron, and Christophe J. Douady

    PLOS One, Aug 2014

    Abs HTML

    This study investigates the genetic divergence of planktonic foraminifera using small subunit ribosomal DNA (SSU rDNA) sequences. The authors analyze a large dataset of SSU rDNA sequences from various species of planktonic foraminifera and assess their genetic divergence. The results show that there is significant genetic divergence among different species, which has implications for understanding the biogeography and evolution of these organisms. The study highlights the importance of molecular techniques in studying planktonic foraminifera and provides a valuable resource for future research in this field.

29. Paleobio

    The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer

    Aurore Andre, Agnes Weiner, Frederic Quillevere, Ralf Aurahs, Raphael Morard, Christophe J. Douady, Thibault de Garidel-Thoron, Gilles Escarguel, Colomban Vargas, and Michal Kucera

    Paleobiology, Win 2013

    Abs HTML

    Previous genetic studies of extant planktonic foraminifera have provided evidence that the traditional, strictly morphological definition of species in these organisms underestimates their biodiversity. Here, we report the first case where this pattern is reversed. The modern (sub)tropical species plexus Globigerinoides sacculifer is characterized by large morphological variability, which has led to the proliferation of taxonomic names attributed to morphological end-members within the plexus. In order to clarify the taxonomic status of its morphotypes and to investigate the genetic connectivity among its currently partly disjunct (sub)tropical populations, we carried out a global survey of two ribosomal RNA regions (SSU and ITS-1) in all recent morphotypes of the plexus collected throughout (sub)tropical surface waters of the global ocean. Unexpectedly, we find an extremely reduced genetic variation within the plexus and no correlation between genetic and morphological divergence, suggesting taxonomical overinterpretation. The genetic homogeneity within the morphospecies is unexpected, considering its partly disjunct range in the (sub)tropical Atlantic and Indo-Pacific and its old age (early Miocene). A sequence variant in the rapidly evolving ITS-1 region indicates the existence of an exclusively Atlantic haplotype, which suggests an episode of relatively recent (last glacial) isolation, followed by subsequent resumption of unidirectional gene flow from the Indo-Pacific into the Atlantic. This is the first example in planktonic foraminifera where the morphological variability in a morphospecies exceeds its rDNA genetic variability. Such evidence for inconsistent scaling of morphological and genetic diversity in planktonic foraminifera could complicate the interpretation of evolutionary patterns in their fossil record.

30. Pal-3

    Ecological modeling of the temperature dependence of cryptic species of planktonic Foraminifera in the Southern Hemisphere

    Raphael Morard, Frederic Quillevere, Gilles Escarguel, Thibault de Garidel-Thoron, Colomban Vargas, and Michal Kucera

    Palaeogeography Palaeoclimatology Palaeoecology, Dec 2013

    HTML
31. Pal-3

    Global scale same-specimen morpho-genetic analysis of Truncorotalia truncatulinoides: A perspective on the morphological species concept in planktonic foraminifera

    Frederic Quillevere, Raphael Morard, Gilles Escarguel, Christophe J. Douady, Yurika Ujiie, Thibault de Garidel-Thoron, and Colomban Vargas

    Palaeogeography Palaeoclimatology Palaeoecology, Dec 2013

    HTML
32. eco&evo

    Longitudinal differentiation among pelagic populations in a planktic foraminifer

    Yurika Ujiie, Takahiro Asami, Thibault de Garidel-Thoron, Hui Liu, Yoshiyuki Ishitani, and Colomban Vargas

    Ecology and Evolution, Jul 2012

    HTML
33. Plos

    Worldwide Genotyping in the Planktonic Foraminifer Globoconella inflata: Implications for Life History and Paleoceanography

    Raphael Morard, Frederic Quillevere, Christophe J. Douady, Colomban Vargas, Thibault de Garidel-Thoron, and Gilles Escarguel

    PLOS One, Oct 2011

    HTML
34. Nature

    Sensitivity of coccolithophores to carbonate chemistry and ocean acidification

    L. Beaufort, I. Probert, T. de Garidel-Thoron, E. M. Bendif, D. Ruiz-Pino, N. Metzl, C. Goyet, N. Buchet, P. Coupel, M. Grelaud, B. Rost, R. E. M. Rickaby, and C. Vargas

    Nature, Aug 2011

    HTML
35. MarMic

    Coiling dimorphism within a genetic type of the planktonic foraminifer Globorotalia truncatulinoides

    Yurika Ujiie, Thibault de Garidel-Thoron, Silvia Watanabe, Peter Wiebe, and Colomban Vargas

    Marine Micropaleontology, Dec 2010

    HTML
36. MarMic

    Morphological recognition of cryptic species in the planktonic foraminifer Orbulina universa

    Raphael Morard, Frederic Quillevere, Gilles Escarguel, Yurika Ujiie, Thibault de Garidel-Thoron, Richard D. Norris, and Colomban Vargas

    Marine Micropaleontology, May 2009

    HTML
37. Paleoc

    A multiproxy assessment of the western equatorial Pacific hydrography during the last 30 kyr

    Thibault de Garidel-Thoron, Yair Rosenthal, Luc Beaufort, Edouard Bard, Corinne Sonzogni, and Alan C. Mix

    Paleoceanography, Jul 2007

    HTML
38. G-cubed

    Low-latitude hydrological cycle and rapid climate changes during the last deglaciation

    Camille Levi, Laurent Labeyrie, Franck Bassinot, Francois Guichard, Elsa Cortijo, Claire Waelbroeck, Nicolas Caillon, Josette Duprat, Thibault de Garidel-Thoron, and Harry Elderfield

    Geochemistry Geophysics Geosystems, May 2007

    HTML
39. GPC

    Late Quaternary paleoceanography of the northwestern Pacific: Results from IMAGES program

    Yair Rosenthal, Thibault de Garidel-Thoron, and Luc Beaufort

    Global and Planetary Change, Aug 2006

    HTML
40. QSR

    Evidence for multiple paleomagnetic intensity lows between 30 and 50 ka BP from a western Equatorial Pacific sedimentary sequence

    CL Blanchet, N Thouveny, and T de Garidel-Thoron

    Quaternary Science Reviews, May 2006

    HTML
41. Nature

    Stable sea surface temperatures in the western Pacific warm pool over the past 1.75 million years

    T de Garidel-Thoron, Y Rosenthal, F Bassinot, and L Beaufort

    Nature, Jan 2005

    HTML
42. PNAS

    Evidence for large methane releases to the atmosphere from deep-sea gas-hydrate dissociation during the last glacial episode

    T de Garidel-Thoron, L Beaufort, F Bassinot, and P Henry

    Proceedings of the National Academy of Sciences of the United States of America, Jun 2004

    HTML
43. MarGeol

    Biomass burning and oceanic primary production estimates in the Sulu Sea area over the last 380 kyr and the East Asian monsoon dynamics

    L Beaufort, T de Garidel-Thoron, B Linsley, D Oppo, and N Buchet

    Marine Geology, Sep 2003

    HTML
44. GPC

    Late quaternary paleoclimatology of the western equatorial Pacific

    Y Rosenthal, T de Garidel-Thoron, DW Oppo, BK Linsley, L Beaufort, F Bassinot, and A Mix

    Global and Planetary Changes, Sep 2003

    HTML
45. Paleoc

    Millennial-scale dynamics of the East Asian winter monsoon during the last 200,000 years

    T de Garidel-Thoron, L Beaufort, BK Linsley, and S Dannenmann

    Paleoceanography, Oct 2001

    HTML
46. Science

    ENSO-like forcing on oceanic primary production during the Late Pleistocene

    L Beaufort, T de Garidel-Thoron, AC Mix, and NG Pisias

    Science, Sep 2001

    HTML