Biblio

Matoušů, A., R. Osudar, K. Šimek, and 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, 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.

Hornak, K., V. Kasalicky, K. Šimek, and 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.

Kasalicky, V., Y. Zeng, K. Piwosz, K. Šimek, H. Kratochvilová, and 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, and 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, and 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, and 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, and 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, and 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

Šimek, K., and 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, and 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, and P. P. Chaudhary. 2019. Study of methane-related processes in sediments along the longitudinal profile of the Elbe River. Limnologica 79: 125716.

Šimek, K., V. Grujčić, I. Mukherjee, V. Kasalický, J. Nedoma, T. Posch, M. Mehrshad, and 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.

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.

Šimek, K., I. Mukherjee, J. Nedoma, C. C. P. Paula, J. Jezberová, D. Sirová, and 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, and 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, and J. Lukeš. 2022. Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory. ISME Journal , doi:10.1038/s41396-022-01192-0