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

Seasonal habitat use of three predatory fishes in a freshwater ecosystem

To understand the spatiotemporal overlap in the habitat use of sympatric predators, we studied longitudinal activity and reservoir section and depth use of pike (Esox lucius), pikeperch (Sander lucioerca) and catfsh (Silurus glanis) in the Římov Reservoir, using an autonomous telemetry system for 11 months. We found signifcant diferences among these species in studied parameters that varied considerably over tracked period. Pike consistently used the same sections of the reservoir, while pikeperch and catfsh frequently visited a tributary during the warm season (late spring and early autumn), and moved closer to the dam during the cold season (late autumn to early spring). Pike longitudinal activity was highest in the cold season, pikeperch in the warm season, and catfsh activity peaked in both seasons. Overlap in the depth use among species was higher in the warm season, when all species used the upper layer of the water column, and lower in the cold season, when pikeperch and catfsh used deeper areas. These results demonstrated overlay and temporal variation of habitat use among these predators, as well as potential spatiotemporal space for their direct ecological interactions. Acoustic telemetry · Predators · Habitat use · Movement ecology · Winter ecologypublishedVersio

Spatial heterogeneity and seasonal succession of phytoplankton on a longitudinal gradient in the Římov reservoir

Spatial distribution and seasonal succesion of phytoplankton along the longitudinal axis of a eutrophic Římov reservoir was investigated in 2007. Inflow, transitional and lacustrine zones were distinquished in the reservoir according to physical, chemical and biological parameters. Using a functional group concept, typical phytoplankton assemblages were found

Application of modern fluorescence techniques in studying growth, viability and phosphatase production of phytoplankton

In this thesis, the modern fluorescence techniques (PDMPO, SYTOX Green and FLEA) coupled with image cytometry were employed to study phytoplankton growth, viability and production of extracellular phosphatases. Seasonal studies at the Římov Reservoir and the Lipno Reservoir were conducted, as well as laboratory experiments

Spatial heterogeneity and seasonal succession of phytoplankton along the longitudinal gradient in a eutrophic reservoir

Spatial distribution and seasonal succesion of phytoplankton along the longitudinal axis of a eutrophic Římov reservoir (Czech Republic) was investigated from April to October 2007, at 1?2 week intervals. Phytoplankton spatial heterogeneity was the most apparent during the summer reflecting a pronounced gradient of environmental parameters from the river inflow to the dam. The riverine zone differed markedly from downstream parts of the reservoir, being dominated by functional groups D and J (large cryptophytes and colonial diatoms). While a dense cyanobacterial bloom (groups H1 and M) occurred in the transition zone, considerably lower biomass of desmids (Group N) was found at lacustrine zone at the same time. A sudden flood event considerably altered nutrient and light availability, and later even resulted in cyanobacterial dominance in the whole reservoir

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes

Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche)

Estimating Environmental Preferences of Freshwater Pelagic Fish Using Hydroacoustics and Satellite Remote Sensing

In this study, a remote sensing-based method of mapping and predicting fish spatial distribution in inland waters is developed. A combination of Earth Observation data, in-situ measurements, and hydroacoustics is used to relate fish biomass distribution and water-quality parameters along the longitudinal transect of the Římov Reservoir (Czech Republic) using statistical and machine learning techniques. Parameter variations and biomass distribution are estimated and validated, and apparent trends are explored and discussed, together with potential limitations and weaknesses. Water-quality parameters exhibit longitudinal gradients along the reservoir, while calculations reveal a distinct fish assemblage pattern observed as a patchy overall biomass distribution. Although the proposed methodology has a great potential for sustainable water management, careful planning is needed to ensure the simultaneous acquisition of remote sensing and in-situ data to maximize calibration accuracy