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Nedoma, J., J. Vrba, J. Hejzlar, K. Šimek, and V. Straskrabova. 1994. N-acetylglucosamine dynamics in freshwater environment: concentration of amino-sugars, extracellular enzyme activities, and microbial uptake. Limnology and Oceanography 39: 1088-1100.

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Šimek, K. 1982. The occurrence of faecal bacteria in a fish pond with a duck farm. Internationale Revue Der Gesamten Hydrobiologie 67: 851-868.

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Hahn, M. W., T. Scheuerl, J. Jezberova, U. Koll, J. Jezbera, K. Šimek, C. Vannini, G. Petroni, and Q. L. Wu. 2012. The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population. PLoS ONE 7: e32772.

Jezbera, J., J. Jezberova, V. Kasalicky, K. Šimek, and M. W. Hahn. 2013. Patterns of Limnohabitans microdiversity across a large set of freshwater habitats as revealed by Reverse Line Blot Hybridization. PLoS ONE 8: e58527.

Straskrabova, V., K. Šimek, M. Macek, P. Hartman, J. Fott, and M. Blazo. 2000. Pelagic food webs and microbial loop in mountain lakes sensitive to acidification W.D. Williams [ed.]. INTERNATIONAL ASSOCIATION OF THEORETICAL AND APPLIED LIMNOLOGY, VOL 27, PT 1, PROCEEDINGS 27: 513-516.

Straskrabova, V., J. Nedoma, K. Šimek, and J. Vrba. 2003. Pelagic microbial assemblages in oligotrophic mountain lakes. Acta Universitatis Ecologiae 10: 15 - 17.

Comerma, M., J. - C. Garcia, J. Armengol, M. Romero, and K. Šimek. 2001. Planktonic food web structure along the Sau Reservoir (Spain) in summer 1997. International Review of Hydrobiology 86: 195-209.

Weinbauer, M. G., J. R. Dolan, and K. Šimek. 2015. A population of giant tailed virus-like particles associated with heterotrophic flagellates in a lake-type reservoir. Aquatic Microbial Ecology 76: 111-116.

Šimek, K., M. Macek, J. Seda, and V. Vyhnalek. 1990. Possible food chain relationships between bacterioplankton, protozoans and cladocerans in a reservoir. Internationale Revue der Gesamten Hydrobiologie 75: 583-596.

Posch, T., K. Šimek, J. Vrba, S. Pernthaler, J. Nedoma, B. Sattler, B. Sonntag, and R. Psenner. 1999. Predator-induced changes of bacterial size-structure and productivity studied on an experimental microbial community. Aquatic Microbial Ecology 18: 235–246.

Pernthaler, J., T. Posch, K. Šimek, J. Vrba, A. Pernthaler, F. O. Glockner, U. Nubel, R. Psenner, and R. Amann. 2001. Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Applied and Environmental Microbiology 67: 2145–2155.

Jezbera, J., K. Hornak, and K. Šimek. 2006. Prey selectivity of bacterivorous protists in different size fractions of reservoir water amended with nutrients. Environmental Microbiology 8: 1330-1339.

Chrzanowski, T. H., and K. Šimek. 1990. Prey-size selection by fresh-water flagellated protozoa. Limnology and Oceanography 35: 1429-1436.

Grujčić, V., V. Kasalicky, and K. Šimek. 2015. Prey-specific growth responses of freshwater flagellate communities induced by morphologically distinct bacteria from the genus Limnohabitans. Applied and Environmental Microbiology 81: 4993–5002.

Dolan, J. R., and K. Šimek. 1997. Processing of ingested matter in Strombidium sulcatum, a marine ciliate (Oligotrichida). Limnology and Oceanography 42: 393-397.

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

Gabaldón, C., M. Devetter, J. Hejzlar, K. Šimek, P. Znachor, J. Nedoma, and 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.

Allers, E., L. Gomez-Consarnau, J. Pinhassi, J. M. Gasol, K. Šimek, and J. Pernthaler. 2007. Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms. Environmental Microbiology 9: 2417–2429.

Šimek, K., and J. Fuksa. 1989. Responses in bacterial activity to changing conditions in plankton - probable controlling mechanisms. Archiv für Hydrobiologie Beihefte Ergebnisse der Limnologie 33: 239-248.

Šimek, K., J. Jezbera, K. Hornak, J. Vrba, and J. Seda. 2004. Role of diatom-attached choanoilagellates of the genus Salpingoeca as pelagic bacterivores. Aquatic Microbial Ecology 36: 257–269.

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Macek, M., C. Callieri, K. Šimek, and A. Lugo Vazquez. 2006. Seasonal dynamics, composition and feeding patterns of ciliate assemblages in oligotrophic lakes covering a wide pH range. Archiv für Hydrobiologie 166: 261-287.

Montagnes, D. J. S., A. B. Barbosa, J. Boenigk, K. Davidson, K. Juergens, M. Macek, J. D. Parry, E. C. Roberts, and K. Šimek. 2008. Selective feeding behaviour of key free-living protists: avenues for continued study. Aquatic Microbial Ecology 53: 83-98.

Šimek, K., P. Kojecka, J. Nedoma, P. Hartman, J. Vrba, and J. R. Dolan. 1999. Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir. Limnology and Oceanography 44: 1634–1644.

Pernthaler, J., K. Šimek, B. Sattler, A. Schwarzenbacher, J. Bobkova, and R. Psenner. 1996. Short-term changes of protozoan control on autotrophic picoplankton in an oligo-mesotrophic lake. Journal of Plankton Research 18: 443-462.

Posch, T., J. Jezbera, J. Vrba, K. Šimek, J. Pernthaler, S. Andreatta, and B. Sonntag. 2001. Size selective feeding in Cyclidium glaucoma (Ciliophora, Scuticociliatida) and its effects on bacterial community structure: A study from a continuous cultivation system. Microbial Ecology 42: 217–227.