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10. Two-Decade Changes in the Ciliate Assemblage Feeding Pattern Reflect the Reservoir Nutrient Load.

Author

Macek, Miroslav, Vrba, Jaroslav, Hejzlar, Josef, Řeháková, Klára, Jarošík, Jiří, Šorf, Michal, and Šimek, Karel

Subjects
AUTUMN, CRYPTOMONADS, BIOMASS, MULTIVARIATE analysis, PLANKTON, CILIATA
Abstract

The perception of the importance of ciliate in freshwater has changed dramatically since the "microbial loop" conceptualisation, reflecting methodological attempts. The data from two decades (1994–2018) on the surface (0–3 m) ciliate assemblage in the Slapy reservoir (Vltava River, Czech Republic) during two different nutrient-load defined periods were analysed. We grouped the identified, quantified, and biomass-evaluated ciliates in the quantitative protargol-impregnated preparations according to their feeding behaviour. The sampling median and interquartile range data of the ciliates were plotted; the modelled water age, nutrients, bacteria, heterotrophic nanoflagellates, and Rhodomonas spp. were applied as the main explanatory background variables. We validated the differences between the periods, engaging multivariate analyses. The picoplankton-filtering species dominated the assemblages in an annual mean (halteriids and minute strobilidiids followed by peritrichs). Algae hunting urotrichs, Balanion planctonicum, and nanoplankton filtering tintinnids were significant before the spring phytoplankton peak when a maximum of ciliate biomass reflected mixotrophic nanoplankton filtering pelagostrombidiids. Only there did ciliate biomass tightly follow their quantified prey. Heterotrophic and mixotrophic Askenasia and Lagynophrya were typical raptorial/flagellate-hunting cilates; only Mesodinium spp. reached the maximum during autumn. The observed oligotrophication of the reservoir increased the ciliate assemblage biomass in the surface layer during stratification in concordance with the Plankton Ecology Group (PEG) model. [ABSTRACT FROM AUTHOR]

Published
2024
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18. High-resolution metagenomic reconstruction of the freshwater spring bloom

Author

Kavagutti, Vinicius S, Bulzu, Paul-Adrian, Chiriac, Cecilia M, Salcher, Michaela M, Mukherjee, Indranil, Shabarova, Tanja, Grujčić, Vesna, Mehrshad, Maliheh, Kasalický, Vojtěch, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Jezberová, Jitka, Seďa, Jaromir, Rychtecký, Pavel, Znachor, Petr, Šimek, Karel, Ghai, Rohit, Kavagutti, Vinicius S, Bulzu, Paul-Adrian, Chiriac, Cecilia M, Salcher, Michaela M, Mukherjee, Indranil, Shabarova, Tanja, Grujčić, Vesna, Mehrshad, Maliheh, Kasalický, Vojtěch, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Jezberová, Jitka, Seďa, Jaromir, Rychtecký, Pavel, Znachor, Petr, Šimek, Karel, and Ghai, Rohit

Abstract

Background: The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce. Results: We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation. Con

Published
2023

20. Additional file 1 of In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model

Author

Park, Hongjae, Shabarova, Tanja, Salcher, Michaela M., Kosová, Lenka, Rychtecký, Pavel, Mukherjee, Indranil, Šimek, Karel, Porcal, Petr, Seďa, Jaromír, Znachor, Petr, and Kasalický, Vojtěch

Abstract

Additional file 1: Figure S1. Box plots for selected physicochemical parameters measured across the sampling stations. Figure S2. Line plots for selected physicochemical parameters measured at the Dam regions of different reservoirs. Figure S3. Two-year vertical distribution of temperature in three reservoirs. Figure S4. Two-year vertical distribution of dissolved oxygen concentration. Figure S5. Rarefaction and species accumulation curves for the 310 samples estimated at oligotype-level. Figure S6. Hierarchical clustering of all samples (n=310). Figure S7. Annual succession patterns of planktonic organisms in reservoir ecosystems during the year 2018. Figure S8. Two-year temporal patterns of the individual bacterial groups from the spring cluster. Figure S9. Two-year temporal patterns of the individual bacterial groups from the clear-water cluster. Figure S10. Two-year temporal patterns of the individual bacterial groups from the summer cluster. Figure S11. Two-year temporal patterns of the individual bacterial groups from the fall/winter cluster.

Published
2023
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34. Start-up Marketing Mix in Relation to Life-Cycle Stage

Author

ŠIMEK, Karel

Subjects
marketing, start-up, životní cyklus, crowdfunding, life cycle
Abstract

The diploma thesis deals with the issue of the start-up life cycle and marketing mix for a chosen start-up. Outlines what is needed for its management and what are the possibilities of a beginning start-up from product development to marketing. The thesis focuses mainly on the definition of the start-up environment. The main objective is to analyze the development of the chosen start-up Adventurer Solutions s.r.o. in the first stages of its life cycle with a focus on the development of the marketing mix and carry out marketing research of target customers through a questionnaire survey and in-depth interviews, verify the concept of a start-up and then implement a crowdfunding campaign to gain the first customers. The work discusses the current marketing mix situation of chosen start-up, marketing procedures within the crowdfunding campaign, both the preparation and marketing activities during it, and offers recommendations for improvements based on the results of the campaign and survey. In conclusion, the thesis deals with the start-up environment in the Czech Republic and summarizes the achieved results.

Published
2021

36. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

Author

Piwosz, Kasia, Mukherjee, Indranil, Salcher, Michaela M., Grujčić, Vesna, and Šimek, Karel

Subjects
CARD-FISH, protists, fungi, aquatic microbial food webs, bacterivorous, heterotrophic and mixotrophic flagellates, Review, grazing by protists, unicellular eukaryotes, omnivorous and predatory flagellates, Microbiology
Abstract

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.

Published
2020

41. CARD‐FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes.

Author

Šimek, Karel, Mukherjee, Indranil, Nedoma, Jiří, de Paula, Caio César Pires, Jezberová, Jitka, Sirová, Dagmara, and Vrba, Jaroslav

Subjects
*FLAGELLATA, *CILIATA, *LAKES, *FRESH water, *OMNIVORES, *MICROBIAL ecology, *IN situ hybridization, *MICROCYSTIS
Abstract

Summary: Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation of key flagellate taxa is currently a major task in microbial ecology. We investigated seasonal changes in the HNF and ciliate community composition as well as taxa‐specific bacterivory in four hypertrophic freshwater lakes. Taxa‐specific catalyzed reporter deposition‐fluorescence in situ hybridization probes assigned taxonomic affiliations to 51%–96% (average ±SD, 75 ± 14%) of total HNF. Ingestion rates of fluorescently labelled bacteria unveiled that HNF contributed to total protist‐induced bacterial mortality rates more (56%) than ciliates (44%). Surprisingly, major HNF bacterivores were aplastidic cryptophytes and their Cry1 lineage, comprising on average 53% and 24% of total HNF abundance and 67% and 21% of total HNF bacterivory respectively. Kinetoplastea were important consumers of bacteria during summer phytoplankton blooms, reaching 38% of total HNF. Katablepharidacea (7.5% of total HNF) comprised mainly omnivores, with changing contributions of bacterivorous and algivorous phylotypes. Our results show that aplastidic cryptophytes, accompanied by small omnivorous ciliate genera Halteria/Pelagohalteria, are the major protistan bacterivores in hypertrophic freshwaters. [ABSTRACT FROM AUTHOR]

Published
2022
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44. A freshwater radiation of diplonemids

Author

Mukherjee, Indranil, primary, Salcher, Michaela M., additional, Andrei, Adrian‐Ştefan, additional, Kavagutti, Vinicius Silva, additional, Shabarova, Tanja, additional, Grujčić, Vesna, additional, Haber, Markus, additional, Layoun, Paul, additional, Hodoki, Yoshikuni, additional, Nakano, Shin‐ichi, additional, Šimek, Karel, additional, and Ghai, Rohit, additional

Published
2020
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