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).
In order to evaluate the effects of contrasting hydrological scenarios on the spatial and temporal heterogeneity of phytoplankton in a reservoir, vertical chlorophyll and temperature profiles were measured and functional classification of phytoplankton was applied. From April to October 2007, at 1-2 week intervals, seasonal changes in various parameters were studied along the longitudinal axis of the canyon-shaped, eutrophic Ř ímov Reservoir (Czech Republic). At the river inflow, phytoplankton markedly differed from the rest of the reservoir, being dominated by functional groups D and J (pennate diatoms and chlorococcal algae) without a clear seasonal pattern. From April to mid-June, groups Y and P (large cryptophytes and colonial diatoms) prevailed in the whole reservoir. Phytoplankton spatial heterogeneity was the most apparent during the summer reflecting a pronounced gradient of environmental parameters from the river inflow to the dam (e.g., decreasing nutrients, increasing light availability, etc.). A dense cyanobacterial bloom (groups H1 and M) developed in the nutrient-rich transition zone, while functional Group N (desmids) dominated the phytoplankton at the same time at the dam area. In late summer, a sudden flood event considerably disrupted thermal stratification, altered nutrient and light availability, and later even resulted in cyanobacterial dominance in the whole reservoir. Additionally, our study emphasizes the importance of having an intensive phytoplankton monitoring program, which would allow for detecting severe consequences of sudden flood events on phytoplankton spatial and temporal heterogeneity, which significantly affect water quality at the dam area used for drinking water purposes.
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.
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