Publications

<<<12345...>>
Total found: 138 records
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
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
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
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
Gabaldon Tebar C., Devetter M., Hejzlar J., Šimek K., Znachor P., Nedoma J., Seďa J. (2019) Seasonal strengths of the abiotic and biotic drivers of a zooplankton community Freshwater Biology 64: 1326–1341.
DOI: 10.1111/fwb.13308
Matoušů A., Rulík M., Tušer M., Bednařík A., Šimek K., Bussmann I. (2019) Methane dynamics in a large river: a case study of the Elbe River Aquatic Sciences 81: UNSP 12.
DOI: 10.1007/s00027-018-0609-9
Šimek K., Grujčić V., Nedoma J., Jezberová J., Šorf M., Matoušů A., Pechar L., Posch T., Bruni E.P., Vrba J. (2019) Microbial food webs in hypertrophic fishponds: Omnivorous ciliate taxa are major protistan bacterivores Limnology and Oceanography 64: 2295–2309.
DOI: 10.1002/lno.11260
Šimek K., Sirová D. (2019) Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems Jove - Journal of Visualized Experiments 151: e59903.
DOI: 10.3791/59903
Weinbauer M., Suominen S., Jezbera J., Kerros M.E., Marro S., Dolan J., Šimek K. (2019) Shifts in cell size and community composition of bacterioplankton due to grazing by heterotrophic flagellates: evidence from a marine system Aquatic Microbial Ecology 83: 295–308.
DOI: 10.3354/ame01919
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
Kasalický V., Zeng Y. H. , Piwosz K., Šimek K., Kratochvilová H., Koblížek M. (2018) Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans Applied and Environmental Microbiology 84: e02116-17.
DOI: 10.1128/AEM.02116-17
Mehrshad M., Salcher M.M., Okazaki Y., Nakano S., Šimek K., Andrei A., Ghai R. (2018) Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome 6: 176.
DOI: 10.1186/s40168-018-0563-8
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
Sirová D., Bárta J., Šimek K., Posch T., Pech J., Stone J., Borovec J., Adamec L., Vrba J. (2018) Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant Microbiome 6 : 225.
DOI: 10.1186/s40168-018-0600-7
Vrba J., Benedová Z., Jezberová J., Matoušů A., Musil M., Nedoma J., Pechar L., Potužák J., Řeháková K., Šimek K., Šorf M., Zemanová J. (2018) Nevstoupíš dvakrát do téhož rybníka – předběžná zpráva o stavu dnešních hypertrofních rybničních ekosystémů [You cannot step into the same fishpond twice – A preliminary report on the current status of hypertrophic fishpond ecosystems] Vodní hospodářství 68 (8): 1-5.
<<<12345...>>

CONTACT

Biology Centre CAS
Institute of Hydrobiology
Na Sádkách 702/7
370 05 České Budějovice

Staff search