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Background Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses. Results Following the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transitions from a homogeneous community to distinct strata-specific communities. A prevalence of auto- and mixotrophic protists dominated by cryptophytes was associated with spring algal bloom-specialized bacteria in the epilimnion. In contrast, the meta- and hypolimnion showcased a development of a protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans, telonemids and excavate protists (Kinetoplastida), co-occurring with bacteria associated with lake snow. Conclusions Our high-resolution sampling matching the typical doubling time of microbes along with the combined microscopic and molecular approach and inclusion of all main components of the microbial food web allowed us to unveil depth-specific populations’ successions and interactions in a deep lentic ecosystem.

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. Con

Heterotrophic nanoflagellates (HNF) are considered as major planktonic bacterivores, however, larger HNF taxa can also be important predators of eukaryotes. To examine this trophic cascading, natural protistan communities from a freshwater reservoir were released from grazing pressure by zooplankton via filtration through 10- and 5-µm filters, yielding microbial food webs of different complexity. Protistan growth was stimulated by amendments of five Limnohabitans strains, thus yielding five prey-specific treatments distinctly modulating protistan communities in 10- versus 5-µm fractions. HNF dynamics was tracked by applying five eukaryotic fluorescence in situ hybridization probes covering 55–90% of total flagellates. During the first experimental part, mainly small bacterivorous Cryptophyceae prevailed, with significantly higher abundances in 5-µm treatments. Larger predatory flagellates affiliating with Katablepharidacea and one Cercozoan lineage (increasing to up to 28% of total HNF) proliferated towards the experimental endpoint, having obviously small phagocytized HNF in their food vacuoles. These predatory flagellates reached higher abundances in 10-µm treatments, where small ciliate predators and flagellate hunters also (Urotricha spp., Balanion planctonicum) dominated the ciliate assemblage. Overall, our study reports pronounced cascading effects from bacteria to bacterivorous HNF, predatory HNF and ciliates in highly treatment-specific fashions, defined by both prey-food characteristics and feeding modes of predominating protists.

High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups, it is advisable to combine HTS with quantification using microscopy and/or the addition of internal standards.

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and CARD-FISH. We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to marine isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single cell genomes of marine diplonemids shows they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.

Despite the importance of shallow lakes worldwide, knowledge of microbial components, the base of their food webs, remains scarce. To close this gap, we investigated planktonic microbial food webs, in particular protistan bacterivory (for both ciliates and heterotrophic nanoflagellates [HNF]), in 10 shallow hypertrophic fishponds in South Bohemia (Czech Republic). We used fluorescently labeled bacteria as bacterivory tracers to estimate how abundant protistan populations in fishponds (4–25 × 103 HNF mL−1 and 55–770 ciliates mL−1) contribute to total bacterial mortality. Fluorescence microscopy, innovative image processing tools, and quantitative protargol staining were combined to detect major bacterivorous and omnivorous ciliate taxa. We quantified bacterial production, bacterivory by individual ciliate species, total ciliates, and total protistan bacterivory in all fishponds. On average, ciliate bacterivory was comparable to that of HNF, accounting for 56% and 44% of total protistan grazing, respectively. We found that primarily bacterivorous Peritrichia (genera Vorticella, Epistylis) and Scuticociliata (Cyclidium spp.) contributed only moderately (mean 26%) to total ciliate bacterivory. Unexpectedly, but highly abundant omnivorous Halteria/Pelagohalteria (Stichotrichia) and, to a lesser extent, also omnivorous Rimostrombidium spp. (Oligotrichia) contributed significantly more (mean 71%) to total ciliate bacterivory than typical bacterivorous taxa. This suggests that unselective grazers, which feed on a broader size spectrum from bacteria to small algae, may have a considerable competitive advantage in hypertrophic environments rich in small particles. Moreover, a meta‐analysis of available literature data supports our hypothesis that the role of ciliate bacterivory increases significantly, relative to HNF bacterivory, along a trophic gradient toward hypertrophic habitats.

Background Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology—the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces. Results Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts. Conclusions We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.

BACKGROUND: Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11. RESULTS: Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway. CONCLUSIONS: Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both

Different bacterioplankton species represent different food quality resources for heterotrophic nanoflagellate (HNF) communities, potentially affecting HNF growth, community dynamics and carbon flow to higher trophic levels. However, our knowledge of such dynamics is still very limited. Here, we describe the results of 11 experiments with natural HNF communities from distinct seasonal phases in two freshwater habitats. The HNF communities were released from predation pressure of zooplankton and incubated with 16 distinct ecologically relevant prey bacterial strains from important Betaproteobacteria genera (Limnohabitans, Polynucleobacter, and Methylopumilus) and one Actinobacteria strain from the Luna 2 cluster. We observed remarkable prey- and season-specific variability in community HNF growth parameters, i.e., doubling time, volumetric gross growth efficiency (GGE), and length of lag phase. All strains, except for the actinobacterium, supported rapid HNF population growth with an average doubling time of 10 h and GGE of 29%. Our analysis revealed that 59% of the variability in flagellate GGE data was explained by the length of lag phase after prey amendments. This indicates a considerable “adaptation time,” during which the predator communities undergo compositional shifts toward flagellate bacterivores best adapted to grow on the offered prey. Importantly, the rapid HNF growth detected on various bacteria tightly corresponds to doubling times reported for fast growing bacterioplankton groups. We propose a conceptual model explaining the tight linkages between rapid bacterial community shifts and succeeding HNF community shifts, which optimize prey utilization rates and carbon flow from various bacteria to the microbial food chain.

We simultaneously studied the impact of top-down (protistan grazing) and bottom-up (phosphorus availability) factors on the numbers and biomasses of bacteria from various phylogenetic lineages, and on their growth and activity parameters in the oligo-mesotrophic Piburger See, Austria. Enhanced grazing resulted in decreased proportions of bacteria with high nucleic acid content (high-NA bacteria) and lower detection rates by FISH. There was a change in the composition of the bacterial assemblage, whereby Betaproteobacteria were heavily grazed while Alphaproteobacteria and Cytophaga—Flavobacterium—Bacteroides were less affected by predators. Changes in bacterial assemblage composition were also apparent in the treatments enriched with phosphorus, and even more pronounced in the incubations in dialysis tubes (allowing relatively free nutrient exchange). Here, Betaproteobacteria became dominant and appeared to act as successful opportunistic competitors for nutrients. In contrast, Actinobacteria did not respond to surplus phosphorus by population growth, and, moreover, maintained their small size, which resulted in a very low biomass contribution. In addition, significant relationships between high-NA bacteria and several bacterial phylogenetic clades were found, indicating an enhanced activity status. By combining several single-cell methods, new insight is gained into the competitive abilities of freshwater bacteria from a variety of phylogenetic lineages under contrasting sets of bottom-up and top-down constraints

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.

Trap fluid of aquatic carnivorous plants of the genus Utricularia hosts specific microbiomes consisting of commensal pro- and eukaryotes of largely unknown ecology. We examined the characteristics and dynamics of bacteria and the three dominant eukaryotes, i.e. the algae-bearing ciliate Tetrahymena utriculariae (Ciliophora), a green flagellate Euglena agilis (Euglenophyta), and the alga Scenedesmus alternans (Chlorophyta), associated with the traps of Utricularia reflexa. Our study focused on ecological traits and life strategies of the highly abundant ciliate whose biomass by far exceeds that of other eukaryotes and bacteria independent of the trap age. The ciliate was the only bacterivore in the traps, driving rapid turnover of bacterial standing stock. However, given the large size of the ciliate and the cell-specific uptake rates of bacteria we estimated that bacterivory alone would likely be insufficient to support its apparent rapid growth in traps. We suggest that mixotrophy based on algal symbionts contributes significantly to the diet and survival strategy of the ciliate in the extreme (anaerobic, low pH) trap-fluid environment. We propose a revised concept of major microbial interactions in the trap fluid where ciliate bacterivory plays a central role in regeneration of nutrients bound in rapidly growing bacterial biomass.

Rivers represent a transition zone between terrestric and aquatic environments, and between methane rich and methane poor environments. The Elbe River is one of the most important rivers draining into the North Sea and, along with the Elbe, a potential importer of high amounts of methane into the water column of the North Sea. Twelve sampling cruises from October 2010 until June 2013 were conducted from Hamburg towards the mouth of the Elbe at Cuxhaven. The dynamic of methane concentration in the water column and its consumption via methane oxidation was measured. In addition, physico-chemical parameters were used to estimate their influence on the methanotrophic activity. We observed high methane concentrations at the stations in the area of Hamburg harbor (“inner estuary”) and about 10 times lower concentrations in the outer estuary (median of 416 versus 40 nmol/L, respectively). The methane oxidation (MOX) rate mirrored the methane distribution with high values in the inner estuary and low values in the outer estuary (median of 161 versus 10 nmol/L/d, respectively). Methane concentrations were significantly influenced by the river hydrology (falling water level) and the trophic state of the water (biological oxygen demand). In contrast to other studies no clear relation to the amount of suspended particulate matter (SPM) was found. Methane oxidation rates were significantly influenced by methane concentration and to a lesser extent by temperature. Methane oxidation accounted for 41 ± 12% of the total loss of methane in the summer/fall, but for only 5 ± 3% of the total loss in the winter/spring. We applied a modified box model taking into account the residence times of each water parcel depending on discharge and tidal impact. We observed almost stable methane concentrations in the outer estuary, despite a strong loss of methane through diffusion and oxidation. Thus, we postulate that the water column undergoes a balancing out in the outer Elbe estuary due to a st

Rivers represent a transition zone between terrestric and aquatic environments, and between methane rich and methane poor environments. The Elbe River is one of the most important rivers draining into the North Sea and, along with the Elbe, a potential importer of high amounts of methane into the water column of the North Sea. Twelve sampling cruises from October 2010 until June 2013 were conducted from Hamburg towards the mouth of the Elbe at Cuxhaven. The dynamic of methane concentration in the water column and its consumption via methane oxidation was measured. In addition, physico-chemical parameters were used to estimate their influence on the methanotrophic activity. We observed high methane concentrations at the stations in the area of Hamburg harbor (“inner estuary”) and about 10 times lower concentrations in the outer estuary (median of 416 versus 40 nmol/L, respectively). The methane oxidation (MOX) rate mirrored the methane distribution with high values in the inner estuary and low values in the outer estuary (median of 161 versus 10 nmol/L/d, respectively). Methane concentrations were significantly influenced by the river hydrology (falling water level) and the trophic state of the water (biological oxygen demand). In contrast to other studies no clear relation to the amount of suspended particulate matter (SPM) was found. Methane oxidation rates were significantly influenced by methane concentration and to a lesser extent by temperature. Methane oxidation accounted for 41 ± 12% of the total loss of methane in the summer/fall, but for only 5 ± 3% of the total loss in the winter/spring. We applied a modified box model taking into account the residence times of each water parcel depending on discharge and tidal impact. We observed almost stable methane concentrations in the outer estuary, despite a strong loss of methane through diffusion and oxidation. Thus, we postulate that the water column undergoes a balancing out in the outer Elbe estuary due to a st

Representative model organisms form the basis on which biology is constructed, and pure cultures offer many opportunities for discovery. However, our view of the importance of axenic cultures changed dramatically at the turn of the last century upon realizing that the majority of environmentally relevant microbes still remains uncultured. The sequencing revolution has led us to a point where we can identify the microbial world in which we live, but many questions remain regarding the autecology of planktonic microbes and their interactions with their environment. Thus, it is essential to isolate and cultivate the key microbial players to gain a deeper insight into their ecology. If the past is a guide, the way forward in confronting the so-called ‘great plate count anomaly’ is the use of more subtle and refined approaches to culturing, using a number of methods and processes that are now becoming available. The vast amount of information accumulated from genome sequencing alone has yet to result in the isolation of the most important and abundant microbes of aquatic systems. We highlight the merits of pure cultures and discuss the critical need to integrate information from a variety of different sources to isolate planktonic microbes. We also describe how to culture bacteria of interest with a full cycle isolation approach based on targeted enrichment and illustrate the benefits of pure cultures with 2 examples of isolated representatives of freshwater Betaproteobacteria.

The competitive strength of four cosmopolitan freshwater betaproteobacterial isolates was investigated in the presence or absence of bacterivorous flagellates during continuous cultivation in artificial minimal medium at two dilution rates. Bacteria reached similar abundance and growth rate in monocultures, but in co-cultures, two strains (Acidovorax sp. and Massilia sp.) displayed significantly higher numbers and growth rates. These potential cross-feeding benefits were also supported by a high nutritional versatility of the two strains. In contrast, Hydrogenophaga sp. was seemingly less competitive or even inhibited by co-cultivation, and Limnohabitans planktonicus displayed striking abundance fluctuations. The latter two strains were least versatile in the uptake of different carbon sources and thus suffered more from interspecific competition. Moreover, remarkable strain-specific responses appeared when bacteria experienced increasing loss rates due to grazing and/or raised dilution rates. Limnohabitans planktonicus developed no successful defence strategy and was close to extinction. Massilia sp. formed grazing-resistant filaments exclusively at low dilution, but was highly reduced at increased flow-through. Acidovorax sp. was selectively ingested, but compensated grazing losses with accelerated growth rates and formed (co-)aggregates together with Hydrogenophaga sp. to escape predation at high flow-through. These species-specific interactions, growth responses and defence strategies strongly modulate mixed microbial assemblages and the microbial food web.

Availability of phosphate for phytoplankton and bacteria and of glucose for bacteria was studied in mesocosms using NW Mediterranean coastal water with added phosphate, glucose, or a combination of both. We observed an initial increase of bacterial production in all mesocosms, a continuous increase of particulate P only in the P-enriched mesocosms, and a greater accumulation of dissolved organic C in the glucose-enriched mesocosms compared to those enriched by both glucose and P. This suggests that the water used was initially P-starved with a certain pool of degradable organic C available for bacteria. Specific phosphate affinities indicated a P limitation for the bacterial community in all mesocosms. Specific glucose affinities were different between the mesocosms but much lower than the theoretical maximum predicted from the diffusion-limited model. This suggests that the glucose pool was not a strong controlling factor of bacterial growth. In the P-enriched mesocosms, it is indicated that the extent of P limitation shifted from highest to lowest, while the available pool of glucose steadily decreased during the experiment. The explanation suggested for these observations is that phosphate regeneration was enhanced in the plankton food web, by which bacterial carbon demand became higher than the degradable organic C produced in the P-enriched mesocosms

We simultaneously studied the impact of top-down (protistan grazing) and bottom-up (phosphorus availability) factors on the numbers and biomasses of bacteria from various phylogenetic lineages, and on their growth and activity parameters in the oligo-mesotrophic Piburger See, Austria. Enhanced grazing resulted in decreased proportions of bacteria with high nucleic acid content (high-NA bacteria) and lower detection rates by FISH. There was a change in the composition of the bacterial assemblage, whereby Betaproteobacteria were heavily grazed while Alphaproteobacteria and Cytophaga—Flavobacterium—Bacteroides were less affected by predators. Changes in bacterial assemblage composition were also apparent in the treatments enriched with phosphorus, and even more pronounced in the incubations in dialysis tubes (allowing relatively free nutrient exchange). Here, Betaproteobacteria became dominant and appeared to act as successful opportunistic competitors for nutrients. In contrast, Actinobacteria did not respond to surplus phosphorus by population growth, and, moreover, maintained their small size, which resulted in a very low biomass contribution. In addition, significant relationships between high-NA bacteria and several bacterial phylogenetic clades were found, indicating an enhanced activity status. By combining several single-cell methods, new insight is gained into the competitive abilities of freshwater bacteria from a variety of phylogenetic lineages under contrasting sets of bottom-up and top-down constraints

Microbial successions were studied in experimental mesocosms of marine water in the presence of additional organic carbon (glucose), phosphorus (P) or both. P addition lead to pronounced blooms of phytoplankton and to significantly enhanced bacterial production. Characteristic succession patterns were observed for two phylogenetic groups of bacteria that both transiently formed > 50% of total cells. An initial bloom of bacteria affiliated to the Alteromonadaceae could not be assigned to any specific treatment and was interpreted as a response to the manipulations during mesocosm set-up. These bacteria rapidly declined with the appearance of heterotrophic nanoflagellates, suggesting a negative effect of selective grazing. The persistence of Alteromonadaceae in the microbial assemblages was significantly favored by the presence of additional glucose. During the second half of the experiment, bacteria affiliated to Rhodobacteriaceae formed a dominant component of the experimental assemblages in treatments with addition of P. The community contribution of Rhodobacteriaceae was significantly correlated with chlorophyll a concentrations only in the P-amended mesocosms (r2 = 0.58). This was more pronounced in the absence of glucose (r2 = 0.85). The phylogenetic and morphological diversity among Rhodobacteriaceae was high, and treatment-specific temporal successions of genotypes related to Rhodobacteriaceae were observed. We suggest that the observed succession patterns reflect different niche preferences: Alteromonadaceae rapidly responded to disturbance and profited from allochthonous glucose input, whereas Rhodobacteriaceae benefited from the phytoplankton bloom. © 2007 The Authors

We simultaneously studied the impact of top-down (protistan grazing) and bottom-up (phosphorus availability) factors on the numbers and biomasses of bacteria from various phylogenetic lineages, and on their growth and activity parameters in the oligo-mesotrophic Piburger See, Austria. Enhanced grazing resulted in decreased proportions of bacteria with high nucleic acid content (high-NA bacteria) and lower detection rates by FISH. There was a change in the composition of the bacterial assemblage, whereby Betaproteobacteria were heavily grazed while Alphaproteobacteria and Cytophaga—Flavobacterium—Bacteroides were less affected by predators. Changes in bacterial assemblage composition were also apparent in the treatments enriched with phosphorus, and even more pronounced in the incubations in dialysis tubes (allowing relatively free nutrient exchange). Here, Betaproteobacteria became dominant and appeared to act as successful opportunistic competitors for nutrients. In contrast, Actinobacteria did not respond to surplus phosphorus by population growth, and, moreover, maintained their small size, which resulted in a very low biomass contribution. In addition, significant relationships between high-NA bacteria and several bacterial phylogenetic clades were found, indicating an enhanced activity status. By combining several single-cell methods, new insight is gained into the competitive abilities of freshwater bacteria from a variety of phylogenetic lineages under contrasting sets of bottom-up and top-down constraints