High-resolution metagenomic reconstruction of the freshwater spring bloom

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. Conclusion We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom

Cell specific primary production of autotrophic and mixotrophic phytoplankton in acidified lakes of the Bohemian Forest.

In 1998, the grain density autoradiography was used to study the primary production of individual species or genera in two acidified lakes (Certovo and Plesne) in the Bohemian Forest (Central Europe). The series of in sittu bottle experiments was conducted in 1999 to examine the effects of phosphorus and carbon enrichments and the base addition on the microbial assemblages.Available from STL Prague, CZ / NTK - National Technical LibrarySIGLECZCzech Republi

Research report on the occurence and composition of autotrophic communities in Lakes Milada and Most.

The limnological measurement and research of periphyton and aquatic macrophytes were conducted in the framework of 'Strategy AV 21, post-mining landscape restoration' in 2020. Despite the good ecological potential in Lakes Milada and Most, there are several indications of possible future deterioration of water quality (e.g., the occurrence of subsurface cyanobacterial maxima in Lake Most, excessive growth of periphyton mats in both lakes, strong bottom anoxia in Lake Milada)

Different effects of planktonic invertebrate predators and fish on the plankton community in experimental mesocosms

The impact of fish and cyclopoid copepod predation on zooplankton communities was evaluated using large-volume mesocosms (depth 9.5 m; volume 13 m3) in the Římov reservoir (Czech Republic). Two yearling roach and perch individuals introduced into mesocosms represented the fish treatment, which was compared to cyclopoid copepods (initial abundance of 2 ind.L−1) and a control with no initial addition of predators. Our results clearly support the hypothesis that planktivorous fish feeding leads to the suppression of large-bodied cladocerans. In the presence of fish, the cladoceran community changed from a dominance of large-bodied Daphnia spp. at the beginning to dominance by the smaller Bosmina longirostris at the end of the experiment. Chlorophyll-a concentration and rotifer abundances increased in the absence of daphnids. In the absence of fish, the presence of large-bodied cladocerans resulted in decreasing chlorophyll-a concentration. Although no significant differences were observed between cyclopoid abundances in treatments stocked with cyclopoids and the control, the proportion of large cladocerans clearly showed the effect of the manipulation. The similar trends in both of these treatments did not confirm the importance of cyclopoid predation in our experiment. The overall strong effect of fish over cyclopoid predation suggests the main role of fish predation in the forming of zooplankton communities and in turn impacting phytoplankton biomass in mesocosms.The impact of fish and cyclopoid copepod predation on zooplankton communities was evaluated using large-volume mesocosms. The overall strong effect of fish over cyclopoid predation suggests the main role of fish predation in the forming of zooplankton communities and in turn impacting phytoplankton biomass in mesocosms

Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach

The ecological relevance and factors shaping dynamics of Limnohabitans sp. have been largely studied by fluorescence in situ hybridization with a 16S rRNA probe targeting the R-BT group (lineages LimBCDE), but not lineage LimA. Consequently, ecology and distribution of LimA remained unknown. We developed a double hybridization strategy using a novel 23S rRNA probe specifically targeting LimA and LimE that in combination with the existing R-BT probe can discriminate LimA populations. This technique was applied for more than 1000 samples from 46 freshwater sites including long-term data sets from oligo-mesotrophic Lake Zurich, CH and meso-eutrophic Římov reservoir, CZ. LimA was ubiquitously distributed and highly abundant. Observed ecological preferences of LimA in Lake Zurich were in general similar to already reported for Limnohabitans with highest numbers in surface waters during growing seasons. Three times higher densities of LimA were detected in Římov reservoir, where they were significantly more abundant at the riverine zone especially after flood events that introduced fresh terrestrial DOM (dissolved organic matter). Moreover, statistical analyses of biological and physicochemical parameters obtained from small dynamic water bodies confirmed a correspondence between LimA and allochthonous DOM, in opposite to R-BT that was more related to algal primary production