Search

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).

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).

Telonemiaare one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedislineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemiain freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situHybridization (CARD-FISH). We recovered Telonemia18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemiaare largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%–20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.

Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we isolated and characterized a cryptophyte virus contributing to the annual collapse of a natural cryptophyte spring bloom population. This viral isolate is also representative for a clade of abundant giant viruses (phylum Nucleocytoviricota) found in freshwaters all over the world.

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 from the 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 (Fluviiciolasp. and Limnohabitansspp.) or even taxonomically narrower populations of Betaproteobacteriaand 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 Limnohabitanscan 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.

Mesocosms represent a helpful tool enabling in situ experiments within the pelagic zone of lakes and reservoirs. Experimental studies using mesocosms are widely used in shallow lakes. Here, we describe an improved method suitable for deep freshwater ecosystems. We use a metal supporting framework carrying four polyethylene bags (circular cross-section, diameter 1.5 m, length 9.5 m). The mesocosm dimensions allow us to test hypotheses covering whole pelagic assemblages including the entire food chain up to fish as the top consumers. The floating construction is light, reusable and inexpensive. The suggested mesocosm design maintains conditions close to those occurring in the adjacent lake water and thus effectively simulates the pelagic environment for various experimental studies.

We used a polyphasic approach combining data from microscopic assessment of fresh biomass and from clone libraries and DGGE fingerprints based on 16S rRNA gene sequences to investigate the cyanobacterial diversity of Czech reservoirs during the summer in 2001 and 2002. A total of 15 genera was identified using the microscopic analysis in 38 samples analysed. They were Anabaena, Anabaenopsis, Aphanizomenon, Aphanocapsa, Aphanothece, Coelomoron, Limnothrix, Merismopedia, Microcystis, Planktolyngbya, Planktothrix, Pseudanabaena, Romeria, Snowella and Woronichinia. We recovered 113 DGGE band sequences from the same samples. In addition, 128 partial 16S rRNA sequences were obtained from two clone libraries of reservoirs Pilská and Orlík. The phylogenetic comparison with the currently available rRNA sequences in databases showed that our sequences belonged to 7 cyanobacterial clusters: Anabaena/Aphanizomenon, Limnothrix, Microcystis, Snowella, Synechococcus, Planktothrix, Woronichinia and a plastid related to Chrysochromulina polylepis (Prymnesiophyceae). Identification of the major populations by the microscopic enumeration and the molecular results were generally congruent (for 32 samples out of 38). Anabaena/Aphanizomenon, Microcystis and Woronichinia were the major genera in the Czech reservoirs during summer, and were present in most of the samples. This study showed some discrepancies between the genera retrieved by the traditional method and the molecular analyses. Differences concerned the presence of minor populations belonging to the genera Aphanothece, Merismopedia, Pseudanabaena, Romeria, Snowella and Synechococcus. These differences can be explained by biases specific to each method (competitive amplification, difficulty to obtain sequences from DGGE bands, problems of microscopic observation of the small-sized genera).

In June and August 1999 bottle experiments examining the effects of phosphorus (P), dissolved inorganic carbon (DIC) enrichment, and pH manipulation (base addition) were conducted in two strongly acidified lakes (Certovo and Plešné) located in the Bohemian Forest (Central Europe). Dinoflagellates and Chrysophytes (only in August) were present in each of the lakes. Chlorophytes and filamentous cyanobacteria were particularly dominant in Plešné Lake. A low concentration of dissolved reactive P (~1 µg l-1) combined with high acid phosphatase activity (2-8 µmol l-1 h-1) and short P turnover time (~2 min) indicated severe P limitation of phytoplankton growth in both of the lakes. After P addition, phytoplankton remained P limited as a consequence of low P availability due to its rapid incorporation into bacterial biomass. With pH treatment primary production was significantly reduced (by ~70%) as a consequence of the hydrogen ion shock effect. Phytoplankton biomass was reduced (by ~20%) as well, as the likely result of P precipitation with aluminium. The experimental DIC addition had no apparent effect on any of the parameters investigated. The experimental treatment did not favor photosynthetic activity of any examined phytoplankton species since there was a simultaneous decrease or increase in photosynthetic activity of all the species studied.

Grain density autoradiography was used to study primary production of individual species or genera in two acidified lakes in the Bohemian Forest (Central Europe). Chrysophytes and dinoflagellates were present in both lakes during the studied season, green algae and filamentous cyanobacteria were observed especially in Plešné Lake. In Certovo Lake, the primary production of Dinobryon pediforme was on average 0.56 µg l-1 h-1 C (38 % of total primary production - PT) at the surface layer and 0.20 µg l-1 h-1 C (25 % of PT) at the metalimnetic depth. Peridinium umbonatum accounted for 27 % of PT(0.65 µg l-1 h-1 C) and 31 % of PT (0.22 µg l-1 h-1 C) at each depth, respectively. In Plešné Lake, Monoraphidium cf. dybowskii comprised an almost identical portion of PT at both layers (63 % of PT). Peridinium accounted for 5-29 % and 1-14 % of PT at each depth. Significant seasonal differences in photosynthetic activity coefficients (PAC; the cell-carbon specific rate of C assimilation) were found as well as differences in PAC between individual species, between the same species in different lakes and in different layers of each lake. The PAC of the mixotrophic bacterivorous Dinobryon was equal or even higher than that of autotrophic species, indicating that it uses ingested bacteria as a source of phosphorus rather than of carbon.