Current research highlights

Genus Limnohabitans - an important freshwater bacterial group serves as a model for testing responses of natural flagellate communities to different bacterial food quality

Interactions between bacterial prey and their predators in freshwater ecosystems are highly complex: For instance, prey-selective grazing of small heterotrophic flagellates on bacteria was found to have significant effects on bacterioplankton community composition. Considerably much less is known about impacts of bacterioplankton community composition (“potential prey food quality effects”) on the predator community composition. Notably, different bacterial strains can have different nutritional value as food for flagellates, thus modulating their growth and community composition and in turn also the overall carbon flow to higher trophic levels.

We proposed an innovative experimental design to examine the influence of prey food quality using four Limnohabitans strains (a key freshwater bacterioplankton group), one Polynucleobacter strain and one actinobacterial strain (Luna 2 cluster) on growth (growth rate, length of lag phase, and growth efficiency) and community composition of a natural flagellate community from a freshwater reservoir. Pyrosequencing of eukaryotic SSU rRNA amplicons was used to assess prey-related changes in flagellate community composition. All Limnohabitans and Polynucleobacter strains were ingested (Figs. 1A to 1J), which yielded significant flagellate community growth. In contrast, the actinobacterial strain did not support the predator growth while its abundance was decreasing and the prey cells were clearly detected in flagellate food vacuoles (Figs. 1K and 1L). Notably, even within the Limnohabitans strains we found significant prey-related differences in flagellate growth parameters, which could not be only related to size or shape of the bacterial prey.

Sequence data characterizing the flagellate communities showed also that not only very different strains but even closely related bacterial prey items induced highly significant differences in the resulting community composition of flagellates. Phylotypes from Chrysophyceae closely related to Pedospumella or Spumella-like subclusters D and E2 were most abundant bacterivorous flagellates rapidly reacting to addition of the bacterial prey of high food quality. Our experimental approaches could provide important insights regarding the question which bacterial strains are active in carbon transfer to the grazer food chain in a particular aquatic system, and which flagellate groups are the key players in the trophic transfer. To our knowledge, the recent study conducted in collaboration with colleagues from Austria, Germany and UK, is the first one clearly documenting strong prey-specific effects of even closely related bacteria on flagellate community composition. This is an ecological aspect that has been long under debate but without any direct evidence concerning natural flagellate assemblages.


Šimek K, Kasalický V, Jezbera J, Horňák K, Nedoma J, Hahn MW, Bass D, Jost S, Boenigk J. 2013: Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria. ISME Journal 7: 1519-1530 (Feature Article, IF = 8.951)



A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring.

We employed high frequency sampling to determine the major factors modulating microbial food-web composition and dynamics through the spring phytoplankton bloom and clear-water phases in a freshwater reservoir. We examined effects of a changing trophic structure of the planktonic community cascading fromthe level of zooplankton, through phytoplankton composition and exudation rates to the level of growth responses and losses to grazers of phylogenetically narrow bacterial lineages. Specific probes for fluorescence in situ hybridization (FISH) revealed important short-lived peaks of genus-like (Fluviiciola sp. and Limnohabitans spp.) or even taxonomically narrower populations of Betaproteobacteria and Flavobacteria (such as FlavB and Flav2 lineages). Protozoan grazing on bacterioplankton was studied by using fluorescently labeled bacteria and by direct analyses of FISH-probe–targeted bacterial phylotypes in flagellate food vacuoles. Evaluations of selective bacterivory, growth responses, and cell biovolumes of various bacterial groups during the spring bloom indicated that certain bacterial groups such as Limnohabitans can contribute to carbon flow to the grazer food chain up to 10-fold more than similarly abundant small cells from the Ac1 lineage of Actinobacteria. During the clear-water phase, filter-feeding cladocera had dominant effects on bacterioplankton abundance and community dynamics, likely through direct grazing on larger bacteria along with altering major substrate pools (via e.g., the herbivores’ sloppy feeding on algae). Fine-temporal resolution data revealed several environmental scenarios, in which the interplay of distinct top-down and bottom-up factors resulted in a competitive advantage of particular bacterial lineages.


Šimek K, Nedoma J, Znachor P, Kasalický V, Jezbera J, Horňák K, Seďa J. 2014: A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring. Limnol. Oceanogr. 59(5): 1477–1492


Biology Centre CAS
Institute of Hydrobiology
Na Sádkách 702/7
370 05 České Budějovice

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