Tanja Shabarova, Ph.D.

Position Job Position: Research Scientist
Department: Department of Aquatic Microbial Ecology (AME)
Workplace: Institute of Hydrobiology

Contact details Phone: 420387775841
E-mail: shabrik@gmail.com
Room: 014

Others Description:

My research explores the fascinating processes underlying the assembly of microbial communities in freshwater ecosystems. By applying metacommunity theory and other ecological frameworks, I aim to identify and explain the successional patterns shaping these communities across temporal and spatial scales. In my current project, my team focuses on Fragilaria crotonensis, a diatom that frequently forms blooms in temperate water bodies. To unravel the intricate interactions within the phycosphere (the microscale environment where bacteria, protists, algae, and fungi coexist) we integrate advanced omics approaches with traditional cell-labeling microscopy techniques. Our work explores the compositional shifts and functional roles of members of these microbial consortia, particularly their contributions to carbon flux and their influence on freshwater food web dynamics.

Research focus

Assembly of microbial communities. Metacommunity theory. Ecology of bacteria and protists in freshwater ecosystems and microbial successions.

CV: Education and Work Experience 01/2021 – till now Researcher at Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS 01/2018 – 12/2020 Associated scientist at Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS Postdoctoral Experience 04/2014 – 2017 Postdoctoral position at Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS 06/2013 – 12/2013 Postdoctoral position at Limnological Station, University of Zurich, Switzerland Awards, Scholarships and Projects (as PI) 2022– 2025 Grant Agency of Czech Republic standard grant 23-05081S, "Hotspot of inter-kingdom interactions: microbial colonization of Fragilaria crotonensis as a model for community assembly processes" 2020 – 2023 Grant Agency of Czech Republic junior grant 20-23718Y, "From dark to dark: do bacterial ‘seeds’ from subsurface habitats find their place in lake hypolimnia?" 2015 – 2016 Support of Perspective Human Resources – Postdoctoral Research program (Czech Academy of Sciences, grant No. L200961502) 2014 Appreciation award for the PhD thesis by Foundation of Limnology and Hydrobiology, Switzerland 2013 Award for young scientists for the PhD thesis (Swiss Commission for Scientific Speleology) 2010 Thomas Bitterli Scholarship for research project on Gallionella bacteria in "F1" cave (Swiss Speleological Society) 2009 – 2010 University of Zurich Candoc Grant No. 57150401 Academic Achievements 12/2008 – 05/2013 PhD thesis at Limnological Station, University of Zurich, Switzerland “Life in subsurface pools: Insight into microbial diversity and dynamics in the endokarst environment”. Supervisor Prof. Jakob Pernthaler 2006 – 2008 MSc Microbiology and Immunology, ETH Zurich, Switzerland Master thesis: “Investigation of bacterioplankton communities in four aquatic karst habitats in two karst caves of Bernese Oberland”. Supervisor Prof. Jakob Pernthaler 2003 – 2006 BSc Microbiology, ETH Zurich, Switzerland 2003 passed ETH Zurich entrance examinations IDs and hyperlinks Researcher ID: B-5327-2015 https://www.webofscience.com/wos/author/record/308346 Scopus ID: 36172727800 https://www.scopus.com/authid/detail.uri?authorId=36172727800 ORCID: 0000-0003-4526-3587 https://orcid.org/0000-0003-4526-3587 Loop profile: 1253087 https://loop.frontiersin.org/people/1253087/overview Current projects 23-05081S Hotspot of inter-kingdom interactions: microbial colonization of Fragilaria crotonensis as a model for community assembly processes The microscale environment of the diatom phycosphere represents a hotspot for inter-kingdom interactions between algae, bacteria, protists and fungi. The diatom Fragilaria crotonensis, owing to its large size and ubiquitous distribution, offers a remarkably suitable model to study such complex and intriguing multi-associations and assembly processes leading to their formation. The recent development in omics techniques in combination with more traditional microscopic cell-labelling methods provide us the opportunity to address these questions at resolution from single algal colony to populations in the natural environment. The proposed research is expected to elucidate on the composition and functions of bacterial members in association with different physiological stages of algae, spatiotemporal changes and presence of protists and fungi. We plan to elaborate on the ecological importance of such consortia in freshwater food webs and achieve better understanding on the modification of carbon fluxes by algae-attached eukaryotes.

Total found: 21 records
Asghar U., Mukherjee I., Sonntag B., Pires de Paula C., Kasalický V., Bulzu P., Singh A., Shabarova T., Piwosz K., Šimek K. (2025) Morphological and molecular analyses of season-specific responses of freshwater ciliate communities to top-down and bottom-up experimental manipulations. mSystems 10: e00304-25. DOI: 10.1128/msystems.00304-25
Fernandez C., Haber M., Layoun P., Chiriac M., Bulzu P., Ghai R., Kasalický V., Shabarova T., Grossart H., Woodhouse J., Piwosz K., Alonso C., Zanetti J., Hamilton D.P., Ngochera M., Nakano S., Okazaki Y., Salcher M. (2025) Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium. Nature Microbiology 10: 2194–2206. DOI: 10.1038/s41564-025-02091-8
Khan S., Wdówka K., Calkiewicz J., Rychert K., Nawrocka L., Ameryk A., Shabarova T., Mukherjee I., Šimek K., Jakubowska A., Zalewski M., Piwosz K. (2025) High-temporal resolution of microbial food web dynamics and structure during phytoplankton blooms in the Baltic Sea Environmental Microbiology 27: e70190. DOI: 10.1111/1462-2920.70190
Salcher M., Layoun P., Fernandez C., Chiriac M., Bulzu P., Ghai R., Shabarova T., Lanta V., Callieri C., Sonntag B., Posch T., Lepori F. , Znachor P., Haber M. (2025) Bringing the uncultivated microbial majority of freshwater ecosystems into culture. Nature Communications 16: 7971. DOI: 10.1038/s41467-025-63266-9
Šimek K., Asghar U., Sonntag B., Kasalický V., Shabarova T., Mukherjee I. (2025) New lineage of scuticociliates dominates the ciliate community and bacterivory in hypolimnetic waters of a freshwater reservoir.. The ISME Journal 19: wraf148. DOI: 10.1093/ismejo/wraf148
Boukheloua R., Mukherjee I., Park H., Šimek K., Kasalický V., Ngochera M., Grossart H., Picazo-Mozo A., Camacho A. , Cabello-Yeves P.J., Rodriguez-Valera F. , Callieri C., Andrei A.S., Pernthaler J., Posch T., Alfreider A., Sommaruga R., Hahn M., Sonntag B., López-García P., Moreira D., Jardillier L., Lepère C., Biderre-Petit C., Bednarska A., Ślusarczyk M., Tóth V.R., Banciu H.L., Kormas K., Orlić S., Śantić D., Muyzer G., Herlemann D.P.R., Tammert H., Bertilsson S., Langenheder S., Zechmeister T. , Salmaso N., Storelli N., Capelli C., Lepori F. , Lanta V., Henriques Vieira H., Kostanjšek F., Kabeláčová K., Chiriac M., Haber M., Shabarova T., Rychtecký P., Fernandez C., Znachor P., Szöke-Nagy T., Layoun P., Wong H., Kavagutti V., Bulzu P., Salcher M., Piwosz K., Ghai R. (2024) Global freshwater distribution of Telonemia protists. The ISME Journal 18: wrae177. DOI: 10.1093/ismejo/wrae177
Mukherjee I., Grujčić V., Salcher M., Znachor P., Seďa J., Devetter M., Rychtecký P., Šimek K., Shabarova T. (2024) Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir. Environmental Microbiome 19: 31. DOI: 10.1186/s40793-024-00574-5
Park H., Bulzu P., Shabarova T., Kavagutti V., Ghai R., Kasalický V., Jezberová J. (2024) Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria. Microbiome 12: 150. DOI: 10.1186/s40168-024-01867-0
Schillé L., Valdés-Correcher E., Archaux F., Balacenoiu F., Bjørn M. C., Bogdziewicz M., Boivin T., Branco M., et al., Mallick S., Mäntylä E., Mårell A., Milanović S., Molnár M., Moreira X., Moser V., Mrázová A., et al., Sam K., Sedikhin N.V., Shabarova T., Tack A.J.M., Thomas R., et al., Varela Z., Barbaro L., Castagneyrol B. (2024) Decomposing drivers in avian insectivory: Large-scale effects of climate, habitat and bird diversity. Journal of Biogeography 51: 1079-1094. DOI: 10.1111/jbi.14808
Schmidt S., Svátková M., Kodeš V., Shabarova T. (2024) Correlations between the increase in atmospheric CO2 and temperature, and the subsequent increase in silica, and groundwater organisms. Science of the Total Environment 955: 176970. DOI: 10.1016/j.scitotenv.2024.176970
Kavagutti V., Bulzu P., Chiriac M., Salcher M., Mukherjee I., Shabarova T., Grujčić V., Mehrshad M., Kasalický V., Andrei A.S., Jezberová J., Seďa J., Rychtecký P., Znachor P., Šimek K., Ghai R. (2023) High‑resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome 11: 15. DOI: 10.1186/s40168-022-01451-4
Park H., Shabarova T., Salcher M., Kosová L., Rychtecký P., Mukherjee I., Šimek K., Porcal P., Seďa J., Znachor P., Kasalický V. (2023) In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model. Microbiome 11: 112. DOI: 10.1186/s40168-023-01522-0
Mujakic I., Andrei A., Shabarova T., Kolesár Fecskeová L., Salcher M., Piwosz K., Ghai R., Koblížek M. (2021) Common presence of phototrophic Gemmatimonadota in temperate freshwater lakes. mSystems 6: e01241-20. DOI: 10.1128/mSystems.01241-20
Shabarova T., Salcher M., Porcal P., Znachor P., Nedoma J., Grossart H., Seďa J., Hejzlar J., Šimek K. (2021) Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession. Nature Microbiology 6: 479–488. DOI: 10.1038/s41564-020-00852-1
Mukherjee I., Salcher M., Andrei A., Kavagutti V., Shabarova T., Grujčić V., Haber M., Layoun P., Hodoki Y., Nakano S., Šimek K., Ghai R. (2020) A freshwater radiation of diplonemids Environmental Microbiology 22: 4658–4668. DOI: doi.org/10.1101/2020.05.14.095992
Piwosz K., Shabarova T., Pernthaler J., Posch T., Šimek K., Porcal P., Salcher M. (2020) Bacterial and eukaryotic small-subunit amplicon data do not provide a quantitative picture of microbial communities, but they are reliable in the context of ecological interpretations mSphere 5: e00052-20. DOI: 10.1128/mSphere.00052-20
Grujčić V., Nuy J. K., Salcher M., Shabarova T., Kasalický V., Boenigk J., Jensen M. , Šimek K. (2018) Cryptophyta as major bacterivores in freshwater summer plankton ISME Journal 12: 1668-1681. DOI: 10.1038/s41396-018-0057-5
Piwosz K., Shabarova T., Tomasch J., Šimek K., Kopejtka K., Kahl S., Pieper D.H. , Koblížek M. (2018) Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) ISME Journal 12: 2640-2654. DOI: 10.1038/s41396-018-0213-y
Šimek K., Grujčić V., Hahn M., Horňák K., Jezberová J., Kasalický V., Nedoma J., Salcher M., Shabarova T. (2018) Bacterial prey food characteristics modulate community growth response of freshwater bacterivorous flagellates Limnology and Oceanography 63: 484–502. DOI: 10.1002/lno.10759
Shabarova T., Kasalický V., Šimek K., Nedoma J., Znachor P., Posch T., Pernthaler J., Salcher M. (2017) Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach Environmental Microbiology 19: 1296–1309 . DOI: 10.1111/1462-2920.13663