Article
Environmental Sciences
Anna Matousu, Martin Rulik, Michal Tuser, Adam Bednarik, Karel Simek, Ingeborg Bussmann
Article
Multidisciplinary Sciences
Karel Simek, Dagmara Sirova
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2019)
Article
Ecology
Markus G. Weinbauer, Saara Suominen, Jan Jezbera, Marie-Emanuelle Kerros, Sophie Marro, John R. Dolan, Karel Simek
AQUATIC MICROBIAL ECOLOGY
(2019)
Article
Limnology
Adam Bednarik, Martin Blaser, Anna Matousu, Michal Tuser, Prem Prashant Chaudhary, Karel Simek, Martin Rulik
Article
Microbiology
Kasia Piwosz, Tanja Shabarova, Jakob Pernthaler, Thomas Posch, Karel Simek, Petr Porcal, Michaela M. Salcher
Article
Microbiology
Karel Simek, Vesna Grujcic, Indranil Mukherjee, Vojtech Kasalicky, Jiri Nedoma, Thomas Posch, Maliheh Mehrshad, Michaela M. Salcher
FEMS MICROBIOLOGY ECOLOGY
(2020)
Article
Microbiology
Indranil Mukherjee, Michaela M. Salcher, Adrian-Stefan Andrei, Vinicius Silva Kavagutti, Tanja Shabarova, Vesna Grujcic, Markus Haber, Paul Layoun, Yoshikuni Hodoki, Shin-ichi Nakano, Karel Simek, Rohit Ghai
ENVIRONMENTAL MICROBIOLOGY
(2020)
Review
Engineering, Environmental
M. Sagova-Mareckova, J. Boenigk, A. Bouchez, K. Cermakova, T. Chonova, T. Cordier, U. Eisendle, T. Elersek, S. Fazi, T. Fleituch, L. Fruhe, M. Gajdosova, N. Graupner, A. Haegerbaeumer, A. -M. Kelly, J. Kopecky, F. Leese, P. Noges, S. Orlic, K. Panksep, J. Pawlowski, A. Petrusek, J. J. Piggott, J. C. S. Rusch, R. Salis, J. Schenk, K. Simek, A. Stovicek, D. A. Strand, M. I. Vasquez, T. Vralstad, S. Zlatkovic, M. Zupancic, T. Stoeck
Summary: The importance and potential of utilizing microbes as bioindicators in water quality monitoring are discussed in this review. Molecular methods have revealed microbial diversity and new metabolic pathways, which can improve our understanding of environmental processes, serving as a solid foundation for novel monitoring programs. Microbial community dynamics are highlighted as a missing link essential for comprehending rapid changes in aquatic ecosystem structure and function, suggesting they should be addressed in future environmental monitoring of freshwater ecosystems.
Review
Microbiology
Kasia Piwosz, Indranil Mukherjee, Michaela M. Salcher, Vesna Grujcic, Karel Simek
Summary: Phagotrophic protists play a crucial role in aquatic food webs, and microscopy-based molecular techniques such as CARD-FISH provide reliable ecological information on specific lineages. Recent findings challenge the simplistic notion that flagellates are predominantly bacterivores, revealing them to be omnivores ingesting prokaryotes and other protists. This suggests a need for an updated model of microbial food webs in pelagic environments, incorporating at least two additional trophic levels in the nanoplankton size fraction.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Tanja Shabarova, Michaela M. Salcher, Petr Porcal, Petr Znachor, Jiri Nedoma, Hans-Peter Grossart, Jaromir Seda, Josef Hejzlar, Karel Simek
Summary: The study shows that flooding events result in washed-out organisms and increased nutrient load, but microbial communities can recover to predisturbance state within two weeks. However, reassembly of phytoplankton and zooplankton takes longer. Dissolved nutrient release is associated with inflow rates and community recovery.
NATURE MICROBIOLOGY
(2021)
Article
Microbiology
Karel Simek, Indranil Mukherjee, Jiri Nedoma, Caio Cesar Pires Paula, Jitka Jezberova, Dagmara Sirova, Jaroslav Vrba
Summary: The study found that aplastidic cryptophytes and ciliates are major protistan bacterivores in hypertrophic freshwater lakes, with HNF contributing more to total protist-induced bacterial mortality rates. During summer phytoplankton blooms, Kinetoplastea also play an important role in consuming bacteria.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Galina Prokopchuk, Tomas Korytar, Valeria Juricova, Jovana Majstorovic, Ales Horak, Karel Simek, Julius Lukes
Summary: Diplonemids are a common group of heterotrophic planktonic microeukaryotes in the world ocean, and they play an important role in marine ecosystems. Research has shown that they can switch dietary patterns and distinguish between food quality and edibility. They possess an opportunistic lifestyle that gives them an advantage in food-limited marine environments.
Article
Ecology
Karel Simek, Indranil Mukherjee, Tiberiu Szoke-Nagy, Markus Haber, Michaela M. Salcher, Rohit Ghai
Summary: Morphologically indistinguishable aplastidic cryptophytes were found to be ubiquitous and prominent protistan bacterivores in freshwater ecosystems, playing important roles in carbon flow. These heterotrophic cryptophytes were generally smaller and more abundant than their chloroplast-bearing counterparts, and their diversity has been largely undiscovered.
Article
Microbiology
Vinicius S. S. Kavagutti, Paul-Adrian Bulzu, Cecilia M. M. Chiriac, Michaela M. M. Salcher, Indranil Mukherjee, Tanja Shabarova, Vesna Grujcic, Maliheh Mehrshad, Vojtech Kasalicky, Adrian-Stefan Andrei, Jitka Jezberova, Jaromir Seda, Pavel Rychtecky, Petr Znachor, Karel Simek, Rohit Ghai
Summary: This study performed high-resolution sampling of the spring bloom in a freshwater reservoir and identified previously unknown microbial taxa using metagenome-assembled genomes. The recovered genomes provide insights into the distributional dynamics and doubling times of microbial lineages during the bloom. Additionally, the study uncovered the presence of aplastidic cryptophytes and giant viruses, offering new understanding of plankton dynamics.