Biblio

Šimek, K., I. Mukherjee, J. Nedoma, C. C. P. Paula, J. Jezberová, D. Sirová, a J. Vrba. 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.

Šimek, K., I. Mukherjee, T. Szöke-Nagy, M. Haber, M. M. Salcher, a R. Ghai. 2022. Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores. The ISME Journal

Prokopchuk, G., T. Korytář, V. Juricová, J. Majstorović, A. Horák, K. Šimek, a J. Lukeš. 2022. Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory. ISME Journal , doi:10.1038/s41396-022-01192-0

Shabarova, T., M. M. Salcher, P. Porcal, J. Nedoma, P. Znachor, H. - P. Grossart, J. Seďa, J. Hejzlar, a K. Šimek. 2021. Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession. Nature Microbiology 6: 479–488.

Šimek, K., V. Grujčić, I. Mukherjee, V. Kasalický, J. Nedoma, T. Posch, M. Mehrshad, a M. M. Salcher. 2020. Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes. FEMS Microbiology Ecology 96: fiaa121.

Šimek, K., a D. Sirova. 2019. Fluorescently labeled bacteria used as a tracer can reveal novel pathways of organic carbon flow in aquatic ecosystems. Journal of Visualized Experiments 151: e59903.

Šimek, K., V. Grujčić, J. Nedoma, J. Jezberova, M. Sorf, A. Matoušů, L. Pechar, T. Posch, E. P. Bruni, a J. Vrba. 2019. Microbial food webs in hypertrophic fishponds: omnivorous ciliate taxa are major protistan bacterivores. Limnology and Oceanography 64: 2295–2309.

Bednařík, A., A. Matoušů, M. Blaser, M. Tušer, M. Rulík, K. Šimek, a P. P. Chaudhary. 2019. Study of methane-related processes in sediments along the longitudinal profile of the Elbe River. Limnologica 79: 125716.

Kasalicky, V., Y. Zeng, K. Piwosz, K. Šimek, H. Kratochvilová, a M. Koblizek. 2018. Aerobic anoxygenic photosynthesis is commonly present within the genus Limnohabitans. Applied and Environmental Microbiology 84: e02116-17.

Šimek, K., V. Grujčić, M. W. Hahn, K. Hornak, J. Jezberová, V. Kasalicky, J. Nedoma, M. M. Salcher, a T. Shabarova. 2018. Bacterial prey food characteristics modulate community growth response of freshwater bacterivorous flagellates. Limnol. Oceanogr , doi:10.1002/lno.10759

Grujčić, V., J. Nuy, M. M. Salcher, T. Shabarova, V. Kasalicky, J. Boenigk, M. Jensen, a K. Šimek. 2018. Cryptophyta as major freshwater bacterivores in experiments with manipulated bacterial prey. ISME

Piwosz, P., T. Shabarova, J. Tomasch, K. Šimek, K. Kopejtka, S. Kahl, D. H. Pieper, a M. Koblizek. 2018. Determining lineage-specific bacterial growth dynamics with a novel approach based on amplicon reads normalization using internal standard (ARNIS). ISME J. 12: 2640-2654.

Mehrshad, M., M. M. Salcher, Y. Okazaki, S. Nakano, K. Šimek, S. A. Andrei, a R. Ghai. 2018. Hidden in plain sight - highly abundant and diverse planktonic freshwater Chloroflexi. Microbiome 176.

Sirova, D., J. Bárta, K. Šimek, T. Posch, J. Pech, J. Stone, J. Borovec, L. Adamec, a J. Vrba. 2018. Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant. Microbiome 225, doi:10.1186/s40168-018-0600-7

Shabarova, T., V. Kasalicky, K. Šimek, J. Nedoma, P. Znachor, T. Posch, J. Pernthaler, a M. M. Salcher. 2017. Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach. Environmental Microbiology 19: 1296–1309.

Šimek, K., G. Pitsch, M. M. Salcher, D. Sirova, T. Shabarova, L. Adamec, a T. Posch. 2017. Ecological Traits of the Algae-Bearing Tetrahymena utriculariae (Ciliophora) from Traps of the Aquatic Carnivorous Plant Utricularia reflexa. Journal of Eukaryotic Microbiology 64: 336-348.

Pitsch, G., L. Adamec, S. Dirren, F. Nitsche, K. Šimek, D. Sirova, a T. Posch. 2017. The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant. Journal of Eukaryotic Microbiology 64: 322-335.

Jezberova, J., J. Jezbera, P. Znachor, J. Nedoma, V. Kasalicky, a K. Šimek. 2017. Limnohabitans genus harbor generalist and opportunist genotype groups: evidence from spatiotemporal succession in a canyon-shaped reservoir. Appl. Environ. Microbiol. 83: e01530-17.

Matoušů, A., R. Osudar, K. Šimek, a I. Bussmann. 2017. Methane distribution and methane oxidation in the water column of the Elbe estuary, Germany. Aquatic Sciences 79: 443-458.

Gabaldón, C., M. Devetter, J. Hejzlar, K. Šimek, P. Znachor, J. Nedoma, a J. Seda. 2017. : Repeated flood disturbance enhances rotifer dominance and diversity in a zooplankton community of a small dammed mountain pond. J. Limnol. 76: 292-304.

Hornak, K., V. Kasalicky, K. Šimek, a H. - P. Grossart. 2017. Strain-specific consumption and transformation of alga-derived dissolved organic matter by members of the Limnohabitans-C and Polynucleobacter-B clusters of Betaproteobacteria. Environ. Microbiol. 19: 4519–4535.

Pitsch, G., L. Adamec, S. Dirren, F. Nitsche, K. Šimek, D. Sirova, a T. Posch. 2016. The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant. Journal of Eukaryotic Microbiology , doi:10.1111/jeu.12369

Salcher, M. M., C. Ewert, K. Šimek, V. Kasalicky, a T. Posch. 2016. Interspecific competition and protistan grazing affect the coexistence of freshwater betaproteobacterial strains. FEMS Microbiology Ecology 92, doi:10.1093/femsec/fiv156

Salcher, M. M., a K. Šimek. 2016. Isolation and cultivation of planktonic freshwater microbes is essential for a comprehensive understanding of their ecology. Aquatic Microbial Ecology 77: 183-196.

Baltar, F., J. Palovaara, F. Unrein, P. Catala, K. Hornak, K. Šimek, D. Vaque, R. Massana, J. M. Gasol, a J. Pinhassi. 2016. Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions. ISME Journal 10: 568-581.