| Total found: 150 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
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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
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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
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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
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Macek M.,
Vrba J.,
Hejzlar J.,
Řeháková K.,
Jarošík J., Šorf M.,
Šimek K. (2024) Two-decade changes in the ciliate assemblage feeding pattern reflect the reservoir nutrient load. Diversity
16: 534.
DOI: 10.3390/d16090534
|
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
|
Šimek K.,
Peterka J.,
Znachor P. (2024) Nevhodná rybářské projekty na horských nádržích Novohradska v povodí vodárenské nádrže Římov. [Inappropriate fishery projects conducted in oligotrophic ponds in Novohradské mountains within the watershed of the Římov drinking water reservoir.] Vodní hospodářství
7-8: 6-11.
|
Vrba J., Šorf M.,
Nedoma J., Benedová Z., Kröpfelová L., Šulcová J., Tesařová B., Musil M., Pechar L., Potužák J., Regenda J.,
Šimek K.,
Řeháková K. (2024) Top‑down and bottom‑up control of plankton structure and dynamics in hypertrophic fishponds. Hydrobiologia
851: 1095–1111.
DOI: 10.1007/s10750-023-05312-5
|
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
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Šimek K.,
Mukherjee I.,
Szöke-Nagy T.,
Haber M.,
Salcher M.,
Ghai R. (2023) Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores. ISME Journal
17: 84–94.
DOI: 10.1038/s41396-022-01326-4
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Prokopchuk G., Korytář T., Juricová V., Horák A., Majstorović J.,
Šimek K., Lukeš J. (2022) Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory The ISME Journal
16: 1409–1419.
DOI: 10.1038/s41396-022-01192-0
Documents to download:
Prokopchuk_2022_ISMEJ (pdf)
|
Šimek K.,
Mukherjee I.,
Nedoma J.,
Pires de Paula C., Jezberová J.,
Sirová D.,
Vrba J. (2022) CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes. Environmental Microbiology
24: 4256–4273.
DOI: 10.1111/1462-2920.15846
|
Piwosz K.,
Mukherjee I.,
Salcher M., Grujčić V.,
Šimek K. (2021) CARD-FISH in the sequencing era: Opening a new universe of protistan ecology. Frontiers in Microbiology
12: 640066.
DOI: 10.3389/fmicb.2021.640066
|
Ságová-Marečková M., Boenigk J., Bouchez A., Cermakova K., Chonova T., Cordier T., Eisendle U., Elersek T., Fazi S., Fleituch T., Frühe L., Gajdosova M., Graupner N., Haegerbaeumer A., Kelly A.-M., Kopecký J., Nõges P., Orlic S., Panksep K., Pawlowski J., Petrusek A., Piggot J.J., Rusch J.C., Salis R., Schenk J.,
Šimek K., Stovicek A., Strand D.A., Vasquez M.I., Vralstad T., Zlatkovic S., Zupancic M., Stoeck T. (2021) Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. Water Research
191: 116767.
DOI: doi.org/10.1016/j.watres.2020.116767
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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
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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
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Šimek K.,
Grujčić V.,
Mukherjee I.,
Kasalický V.,
Nedoma J., Posch T.,
Mehrshad M.,
Salcher M. (2020) Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes FEMS Microbiology Ecology
96: fiaa121.
DOI: doi.org/10.1093/femsec/fiaa121
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Bednařík A., Blaser M.,
Matoušů A.,
Tušer M., Chaudhary P.P. ,
Šimek K., Rulík M. (2019) Sediment methane dynamics along the Elbe River Limnologica
79: 125716.
DOI: 10.1016/j.limno.2019.125716
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