Biogeosystem Modelling Group (BIOGEO)

Coordinator:  Prof. dr hab. Jarosław Tyszka 
           Instytut Nauk Geologicznych PAN
           Ośrodek Badawczy w Krakowie  
           ( Institute of Geological Sciences P.A.S., Research Centre in Kraków )
           ul. Senacka 1,   31-002 Kraków
Phone:  (48) 12 3705 200 ; 12 422-89-20 ; Ext.: 216 
             (48) 12 3705 216 

Fax: (48) 12 3705 205 ; 12 422-16-09

         BIOGEO interdisciplinary research team investigates natural multiscale processes occurring at the interface of the biosphere and the geosphere with the special focus on marine paleo/environments.These processes are analyzed at various spatio-temporal scales, ranging from molecular to global phenomena that last from milliseconds to millions of years. The principal aim is to apply multiscale approach as the key to reconstruct the past and predict future ecosystem changes. This research is based on novel and classical methods, including in fossilio, in vivo and in silico approaches. Microfossil remains of Dinoflagellata and Foraminifera are applied as tools for biostratigraphy and paleoenvironmental reconstructions, including e.g. palaeobathymetry, relative sea-level changes, palaeogeography, marine paleocirculation, as well as interpretations of temperature, salinity, and pH trends. An actualistic approach is also used to study morphogenetic and biomineralization mechanisms in Foraminifera. Our equipment is designed to culture, observe and run experiments on living foraminifera and other micro-organisms applied as environmental indicators. The in silico research is based on the geosystem modelling, applied to paleoclimate and paleoceanographic simulations based on geological proxies. The team cooperates with IT researchers in order to implement morphogenetic and microhabitat models for testing empirical results.



1. Micropalaeontological indicators of palaeoenvironments
2. Morphogenesis and biomineralization of foraminifera
3. Multi-scale modeling of foraminifera
4. Modeling of the Earth system

Team composition:

  1. MSc. Karolina Godos-  PhD student
  2. MSc. Jan Goleń - Technician
  3. Dr  Agata Jarzynka Research Specialist
  4. Dr  Michael Lintner Post-doc / Assistant Professor 
  5. Dr Igor Niezgodzki - Assistant Professor
  6. Dr Wiesława Radmacher - Assistant Professor
  7. Prof. Dr habil. Jarosław Tyszka  -  Group leader/coordinator


  1. Actualistic Experimental Lab
  2. Computer Modelling Lab



                     Publications (BioGeo)


  • Godos K., Tyszka J., Radmacher W., Goleń J. (2021). Global Database of Foraminiferal Organic Linings: ForamL Version 1.2. Mendeley Data.
  • Goleń J., Tyszka J. & Godos K. (2021). Fluorescent double labelling of F-actin in Foraminifera: evaluation of granular pattern F-actin organisation in reticulopodia. Biogeosciences Discussions, 1-14.
  • Lunt D.J., Bragg F., Chan W.L., Hutchinson D.K., Ladant J.B., Morozova P., Niezgodzki I., Steinig S, Zhang Z, Zhu J., Abe Ouchi A., Anagnostou E., deBoer A.M., Coxall H.K., Donnadieu Y., Foster G., Inglis G.N., Knorr G., Langebroek P.M., Lear C.G., Lohmann G., Poulsen Ch.J., Sepulchre P., Tierney J.E., Valdes P.J., Volodin E.M., Dunkley Jones T., Hollis Ch.J., Huber M., Otto-Bliesner B.L. (2021). DeepMIP: Model intercomparison of early Eocene climatic optimum (EECO) large-scale climate features and comparison with proxy data. Climate of the Past17(1), 203-227.
  • Radmacher W., Vásquez O.J., Tzalam M., Jolomná M., Molineros A. Eldrett J. S. (2021). What happened to the organic matter from the Upper Cretaceous succession in Guatemala, Central America? Marine and Petroleum Geology133, 105246.

  • Tyszka J., Godos K., Goleń J.Radmacher W. (2021). Foraminiferal organic linings: Functional and phylogenetic challenges. Earth-Science Reviews, 103726. 


  • Goleń J., Tyszka J., Bickmeyer U., Bijma J. (2020). SiR-actin-labelled granules in foraminifera: patterns, dynamics, and hypotheses. Biogeosciences17(4), 995-1011. 
  • Klages J.P., Salzmann U., Bickert T., Hillenbrand C.-D., Gohl K., Kuhn G., Bohaty S.M., Titschack J., Müller J., Thomas Frederichs T., Bauersachs T., Ehrmann W., van de Flierdt T., Pereira P.S., Larter R.D., Lohmann G., Niezgodzki I., Uenzelmann-Neben G., Zundel M., Spiegel C., Mark C., Chew D., Francis J.E., Nehrke G., Schwarz F., Smith J.A., Freudenthal T., Esper O., Pälike H., Ronge T.A., Dziadek R. (2020). Temperate rainforests near the South Pole during peak Cretaceous warmth. Nature, 580(7801), 81-86.
  • Nowicka A., Tokarz B., Zwyrtková J., Dvořák Tomaštíková E., ProcházkováK., Ercan U., Finke A., Rozhon W., Poppenberger B.,
    Otmar M., Niezgodzki I.,  Krečmerová M.,  Schubert I., Pecinka A. (2020). Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage. The Plant Journal, 102(1), 68-84.
  • Radmacher W., Kobos K., Tyszka J., Jarzynka A., Arz J.A. (2020). Palynological indicators of palaeoenvironmental perturbations in the Basque-Cantabrian Basin during the latest Cretaceous (Zumaia, northern Spain). Marine and Petroleum Geology112, 104107. 
  • Radmacher W., Uchman A. (2020). Oxygen as a factor controlling palynological record: An example from the Cenomanian–Turonian transition in the Rybie section, Polish Carpathians. Marine and Petroleum Geology112, 104067.
  • Radmacher W., Niezgodzki I., Tyszka J., Mangerud G., Pearce, M.A. (2020). Palynology vs. model simulation: oceanographic reconstruction of incomplete data from the Cretaceous Greenland–Norwegian Seaway. Newsletters on Stratigraphy, 93-120. doi.org10.1127/nos/2019/0527


  • Frontalini F., Losada M.T., Toyofuku T., Tyszka J., Goleń J., de Nooijer L., Ikuta T. (2019). Foraminiferal ultrastructure: a perspective from fluorescent and fluorogenic probes. Journal of Geophysical Research: Biogeosciences124(9), 2823-2850.
  • Goleń J., Tyszka J., Bickmeyer U., Bijma J. (2019). Dynamics and organization of actin-labelled granules as a rapid transport mode of actin cytoskeleton components in Foraminifera. Biogeosciences Discussions, 1-25.
  • Niezgodzki I., Knorr G., Tyszka J., Lohmann G. (2019). Extremely low seasonality in the Late Cretaceous Arctic Ocean simulated by the Earth system model. In Geophysical Research Abstracts (Vol. 21).
  • Niezgodzki I., Tyszka J., Knorr G., Lohmann G. (2019). Was the Arctic Ocean ice free during the latest Cretaceous? The role of CO2 and gateway configurations. Global and planetary change177, 201-212.
  • Radmacher W., Niezgodzki I., Tyszka J., Mangerud G., Pearce M.A. (2019). Palynology vs. model simulation: oceanographic reconstruction of incomplete data from the Cretaceous Greenland–Norwegian Seaway. Newsletters on Stratigraphy
  • Stap L.B., Knorr G., Sutter J., Niezgodzki I., Lohmann G. (2019). Modeled difference between the Oligocene and Miocene Antarctic ice sheet. In Geophysical Research Abstracts (Vol. 21).
  • Tyszka J., Bickmeyer U., Raitzsch M., Bijma J., Kaczmarek K., Mewes A., Janse M. (2019). Form and function of F-actin during biomineralization revealed from live experiments on foraminifera. Proceedings of the National Academy of Sciences116(10), 4111-4116.


  • Bojanowski M.J., Ciurej A., Haczewski G., Jokubauskas P., Schouten S., Tyszka J., Bijl P.K. (2018). The Central Paratethys during Oligocene as an ancient counterpart of the present-day Black Sea: Unique records from the coccolith limestones. Marine Geology403, 301-328.
  • Nagai Y., Uematsu K., Chen C., Wani R., Tyszka J., Toyofuku T. (2018). Weaving of biomineralization framework in rotaliid foraminifera: implications for paleoceanographic proxies. Biogeosciences15(22), 6773. 
  • Vahlenkamp M., Niezgodzki I., De Vleeschouwer D., Lohmann G., Bickert T., Pälike H. (2018). Ocean and climate response to North Atlantic seaway changes at the onset of long-term Eocene cooling. Earth and Planetary Science Letters, 498, 185-195.
  • Vahlenkamp M., Niezgodzki I., De Vleeschouwer D., Bickert T., Harper D., Turner S.K., Pälike H. (2018). Astronomically paced changes in deep-water circulation in the western North Atlantic during the middle Eocene. Earth and Planetary Science Letters484, 329-340.
  • Razmjooei M.J., Thibault N., Kani A., Dinarès-Turell J., Pucéat E., Shahriari S., Radmacher W., Jamali A.,M., Ullmann C., Voigt S., Cocquerez T. (2018). Integrated bio-and carbon-isotope stratigraphy of the Upper Cretaceous Gurpi Formation (Iran): A new reference for the eastern Tethys and its implications for large-scale correlation of stage boundaries. Cretaceous Research, 91, 312-340. doi.org10.1016/j.cretres.2018.07.002


  • Barbacka M., Pacyna G., Kocsis Á.T., Jarzynka A., Ziaja J., Bodor E. (2017). Changes in terrestrial floras at the Triassic-Jurassic Boundary in Europe. Palaeogeography, Palaeoclimatology, Palaeoecology480, 80-93.
  • Komosinski M., Mensfelt A., Tyszka J., Goleń J. (2017). Multi-agent simulation of benthic foraminifera response to annual variability of feeding fluxes. Journal of computational science21, 419-43.
  • Niezgodzki I., Knorr G., Lohmann G., Tyszka J., Markwick P.J. (2017). Late Cretaceous climate simulations with different CO2 levels and subarctic gateway configurations: A model‐data comparison. Paleoceanography32(9), 980-998.
  • Niezgodzki I., Knorr G., Lohmann G., Tyszka J. (2017). Impact of Northern Hemisphere polar gateways on the Arctic Ocean climate during the latest Cretaceous as simulated by an Earth System Model. In EGU General Assembly Conference Abstracts (Vol. 19, p. 3220).
  • Radmacher W., Tyszka J., Mangerud G., Pearce M. (2017). Dinoflagellate cyst biostratigraphy of the Upper Cretaceous succession in the sub-Arctic region. In EGU General Assembly Conference Abstracts (Vol. 19, p. 7745).
  • Radmacher W., Niezgodzki I., Setoyama E., Tyszka J., Mangerud G., Kaminski M.A., Lohmann G. (2017). Freshwater forcing on the greenhouse Arctic climate in the Late Cretaceous: Implications from proxies and model simulations.In EGU General Assembly Conference Abstracts (Vol. 19, p. 7945).
  • Topa P., Faber Ł., Tyszka J., Komosinski M. (2017). Modelling ecology and evolution of Foraminifera in the agent-oriented distributed platform. Journal of Computational Science18, 69-84.
  • Setoyama E., Kaminski M., Tyszka J. (2017). Late Cretaceous–Paleogene foraminiferal morphogroups as palaeoenvironmental tracers of the rifted Labrador margin, northern proto-Atlantic. Grzybowski Foundation Special Publication22, 179-220.
  • Vahlenkamp M., Niezgodzki I., De Vleeschouwer D., Bickert T., Harper D., Lohmann G., Zachos J.C. (2017). Astronomically paced middle Eocene deepwater circulation in the western North Atlantic. In EGU General Assembly Conference Abstracts (Vol. 19, p. 15725).
  • Walliser E.O., Lohmann G., Niezgodzki I., Schöne B.R. (2017). Inter-annual climate variability in Europe during the Oligocene icehouse. Palaeogeography, Palaeoclimatology, Palaeoecology475, 140-153.
  • Walliser E.O., Lohmann G., Niezgodzki I., Tütken T., Schöne B.R. (2016). Response of Central European SST to atmospheric pCO2 forcing during the Oligocene–A combined proxy data and numerical climate model approach. Palaeogeography, Palaeoclimatology, Palaeoecology, 459, 552-569, doi:10.1016/j.palaeo.2016.07.033


  • Jarzynka A. (2016). Fossil flora of Middle Jurassic Grojec clays (southern Poland). Raciborski’s original material reinvestigated and supplemented. II. Pteridophyta. Osmundales. Acta Palaeobotanica56(2), 183-221.
  • Komosinski M., Mensfelt A., Topa P., Tyszka J. (2016). Application of a morphological similarity measure to the analysis of shell morphogenesis in Foraminifera. In Man–Machine Interactions 4 (pp. 215-224). Springer, Cham.
  • Walliser E.O., Lohmann G., Niezgodzki I., Tütken T., Schöne B.R. (2016). Response of Central European SST to atmospheric pCO2 forcing during the Oligocene–A combined proxy data and numerical climate model approach. Palaeogeography, Palaeoclimatology, Palaeoecology459, 552-569.


  • Jarzynka A., Pacyna G. (2015). Fossil flora of Middle Jurassic Grojec clays (southern Poland). Raciborski’s original material reinvestigated and supplemented. I. Sphenophytes. Acta Palaeobotanica, 55(2), 149-181.
  • Lohmann G., Niezgodzki I., Knorr G., Tyszka J., Markwick P. (2015). Climate sensitivity under present and Late Cretaceous background conditions. In EGU General Assembly Conference Abstracts (Vol. 17).
  • Niezgodzki I., Knorr G., Lohmann G., Tyszka J. (2015). Impact of marine gateways on the Northern Hemisphere polar climate in the Late Cretaceous as simulated by an Earth System Model. In EGU General Assembly Conference Abstracts (Vol. 17).
  • Radmacher W.,Mangerud G., Tyszka J. (2015). Dinoflagellate cyst biostratigraphy of Upper Cretaceous strata from two wells in the Noegian Sea. Review of Palaeobotany and Palynology216, 18-32.
  • Tyszka J., Raitzsch M., Bijma J., Höher N., Bickmeyer U., Rivera-Ingraham G., Travis J. (2015). Morphogenetic role of F-actin meshwork in chamber formation: immunolabeling results from symbiont bearing benthic foraminifera. In EGU General Assembly Conference Abstracts (Vol. 17). 


  • Barbacka M., Bodor E., Jarzynka A., Kustatscher E., Pacyna G., Popa M.E., Ziaja J. (2014). European Jurassic floras: statistics and palaeoenvironmental proxies. Acta Palaeobotanica54(2), 173-195.
  • Krupnik J., Ziaja J., Barbacka M., Feldman-Olszewska A., Jarzynka A. (2014). A palaeoenvironmental reconstruction based on palynological analyses of Upper Triassic and Lower Jurassic sediments from the Holy Cross Mountains region. Acta Palaeobotanica54(1), 35-65.
  • Radmacher W., Tyszka J., Mangerud G. (2014). Distribution and biostratigraphical significance of Heterosphaeridium bellii sp. nov. and other Late Cretaceous dinoflagellate cysts from the southwestern Barents Sea. Review of Palaeobotany and Palynology, 201, 29-40.
  • Radmacher W., Pérez-Rodríguez I., Arz J.A., Pearce M.A. (2014). Dinoflagellate biostratigraphy at the Campanian-Maastrichtian boundary in Zumaia, northern Spain. Cretaceous Research51, 309-320.
  • Radmacher W., Tyszka J., Mangerud G., Pearce M.A. (2014). Dinoflagellate cyst biostratigraphy of the Upper Albian to Lower Maastrichtian in the southwestern Barents Sea. Marine and Petroleum Geology 57, 109-121. doi.org10.1016/j.marpetgeo.2014.04.008


  • Pawlowski J., Holzmann M., Tyszka J. (2013). New supraordinal classification of Foraminifera: Molecules meet morphology. Marine Micropaleontology, 100, 1-10.
  • Setoyama E., Radmacher W., Kaminski M.A., Tyszka J. (2013). Foraminiferal and palynological biostratigraphy and biofacies from a Santonian–Campanian submarine fan system in the Vøring Basin (offshore Norway). Marine and Petroleum geology, 43, 396-408.


  • Hart M.B., Hudson W., Christopher W., Smart C.W., Tyszka J. (2012). A reassessment of 'Globigerina bathoniana' Pazdrowa, 1969 and the palaeoceanographic significance of Jurassic planktic foraminifera from southern Poland. Journal of Micropalaeontology 31(1): 97-109.
  • Topa P., Tyszka J., Bowser S.S., Travis J.L. (2012). DPD model of foraminiferal chamber formation: simulation of actin meshwork - membrane interactions. Lecture Notes in Computer Science (LNCS), Springer-Verlag Berlin Heidelberg, 669-678.
  • Tyszka J. (2012). Bartensteinites campanulatus nov. gen, nov. sp. - functional morphology of a new foraminiferal genus from the Albian of the Lower Saxony Basin. Neues Jahrbuch für Geologie und Paläontologie - Abhandlungen, Vol. 266 (3): 273-282.


  • Cetean C.G., Setoyama E., Kaminski M.A., Neagu T., Bubík M., Filipescu S., Tyszka J. (2011). Eobigenerina, a cosmopolitan deep-water agglutinated foraminifer, and remarks on late Paleozoic to Mesozoic species formerly assigned to Pseudobolivina and Bigenerina. In: Kaminski, M.A., Filipescu, S. (Eds), Proceedings of the Eighth International Workshop on Agglutinated Foraminifera. Grzybowski Foundation Special Publication, 16, pp. 19-27.
  • Kaminski M.A., Cetean C.G., Tyszka J. (2011). Nomenclature to describe the transition from multiserial to uniserial chamber arrangement in benthic foraminifera. Journal of Micropalaeontology 30(1): 7-10.
  • Setoyama E., Kaminski M.A., Tyszka J. (2011). Late Cretaceous agglutinated foraminifera and implications for the biostratigraphy and palaeobiogeography of the southwestern Barents Sea. In: Kaminski, M.A., Filipescu, S. (Eds), Proceedings of the Eighth International Workshop on Agglutinated Foraminifera. Grzybowski Foundation Special Publication 6, pp. 251-309.
  • Setoyama E., Kaminski M.A., Tyszka J. (2011). A study of Campanian agglutinated foraminifera from the Lomonosov Ridge, IODP Leg 302, ACEX, in the paleogeographic context of the Arctic. Micropalentology 57, no. 6: 507-530.
  • Topa P., Tyszka J., Bowser S.S.,Travis J.L. (2011). DPD model of foraminiferal chamber formation: simulation of actin meshwork–plasma membrane interactions. In International Conference on Parallel Processing and Applied Mathematics (pp. 588-597). Springer, Berlin, Heidelberg.


  • Tyszka J., Jach R., Bubík M. (2010). Recurvoides infernus: a new vent-related foraminifer from the Lower Toarcian black claystone of the Tatra Mountains, Poland. Acta Palaeontologica Polonica 55 (2): 333-342.