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Eutrophication and lake depth are of key importance in structuring lake ecosystems. To elucidate the effect of contrasting nutrient concentrations and water levels on the microbial community in fully mixed shallow lakes, we manipulated water depth and nutrients in a lake mesocosm experiment in north temperate Estonia and followed the microbial community dynamics over a 6-month period. The experiment was carried out in Lake Võrtsjärv—a large, shallow eutrophic lake. We used two nutrient levels crossed with two water depths, each represented by four replicates. We found treatment effects on the microbial food web structure, with nutrients having a positive and water depth a negative effect on the biomasses of bacterial and heterotrophic nanoflagellates (HNF) (RM-ANOVA, p < 0.05). Nutrients affected positively and depth negatively the mean size of individual HNF and ciliate cells (RM-ANOVA; p < 0.05). The interactions of depth and nutrients affected positively the biomass of bacterivorous and bacteri-herbivorous ciliates and negatively the biomass of predaceous ciliates (RM-ANOVA; p < 0.05). Bacterivorous ciliates had lowest biomass in shallow and nutrient-rich mesocosms, whilst predaceous ciliates had highest biomass here, influencing trophic interactions in the microbial loop. Overall, increased nutrient concentrations and decreased water level resulted in an enhanced bacterial biomass and a decrease in their main grazers. These differences appeared to reflect distinctive regulation mechanisms inside the protozoan community and in the trophic interactions in the microbial loop community.

Photoautotrophic picoplankton (0.2–2 μm) can be a major contributor to primary production and play a significant part in the ecosystem carbon flow. However, the understanding about the dynamics of both eukaryotic and prokaryotic components of picoplankton in shallow eutrophic freshwater environments is still poor. Very few studies in these ecosystems reveal the taxonomic composition of picoeukaryotes. The main objective of this study was to investigate the seasonal dynamics of phototrophic picoplankton with the emphasis on the eukaryote community composition in a large shallow, eutrophic lake of the northern temperate zone (Lake Võrtsjärv). Phytoplankton pigments were employed to determine the taxonomic composition of photoautotrophic picoplankton. We found out that photoautotrophic picoplankton constitutes an important part of the phytoplankton community in Lake Võrtsjärv and its contribution can be highly variable (from ~9.3% to ~39%) in different years. The eukaryotic photoautotrophic picoplankton was dominated by diatoms followed by chrysophytes and other minor groups. Picoeukaryotes were prevailing in low-light conditions and low temperatures as their predominance in the picoplankton community was tightly linked to the presence or absence of ice cover. Ice cover strongly suppressed the growth of picocyanobacteria. Total phosphorus, turbidity and metazooplankton abundance had a clear relationship with photoautotrophic picoplankton chlorophyll a.

We numerically explored the effects of long-term water level changes on biotic biomass and spatial distribution of fish in a large shallow lake. We calibrated Ecospace model (Ecopath with Ecosim modelling suite) with data from various functional groups (ranging from phytoplankton to piscivorous fish), and considered 14 different habitats. Two scenarios representing, respectively, a long-term water-level increase and decrease by 1 m were constructed and run for a period of thirty eight years (1979–2016). The results showed a very uneven spatial distribution of fish biomass in the lake, with the highest con- centration in the southern basin. The 1 m decrease scenario caused a diminution in the biomass of all groups but piscivorous fish. The 1 m increase scenario saw a weak decrease in most species biomass. Consequently, in both scenarios, long-term water level changes would be generally detrimental to the lake biota. In the context of more frequent climate-induced hydrological fluctuations, we encourage the use of these simulations as effective tools for future prediction and assessment of ecosystem-based fisheries management and ecological status maintenance of shallow lakes. This research was supported by Estonian Research Council grant PSG32 to FC and UB, by Environmental Investment Center project-T180209PKKH, by IUT 21-2 of the Estonian Ministry of Education and by European Union Regional Development Fund program DoRa+ and ASTRA. This research was supported by Estonian Research Council grant PSG32 to FC and UB, by Environmental Investment Center project-T180209PKKH, by IUT 21-2 of the Estonian Ministry of Education and by European Union Regional Development Fund program DoRa+ and ASTRA.

We aimed to investigate the influence of environmental factors and predict zooplankton biomass and abundance in shallow eutrophic lakes. We employed time series of zoo- plankton and environmental parameters that were measured monthly during 38 years in a large, shallow eutrophic lake in Estonia to build estimates of zooplankton community metrics (cladocerans, copepods, rotifers, ciliates). The analysis of historical time series revealed that air temperature was by far the most important variable for explaining zooplankton biomass and abundance, followed, in decreasing order of importance, by pH, phytoplankton biomass and nitrate concentration. Models constructed with the best predicting variables explained up to 71% of zooplankton biomass variance. Most of the predictive variables had opposing or antagonistic interactions, often mitigating the effect of temperature. In the second part of the study, three future climate scenarios were developed following different Intergovernmental Panel on Climate Change (IPCC) tem- perature projections and entered into an empirical model. Simulation results showed that only a scenario in which air temperature stabilizes would curb total metazooplankton biomass and abundance. In other scenarios, metazooplankton biomass and abundance would likely exceed historical ranges whereas ciliates would not expand. Within the metazooplankton community, copepods would increase in biomass and abundance, whereas cladocerans would lose in biomass but not in abundance. These changes in the zooplankton community will have important consequences for lake trophic structure and ecosystem functioning. This research was supported by the Estonian Research Council Grants PSG32, PRG709 and institutional research funding IUT 21-2 of the Estonian Ministry of Education and Research. This research was supported by the Estonian Research Council Grants PSG32, PRG709 and institutional research funding IUT 21-2 of the Estonian Ministry of Education and Research.

Important drivers of gross primary production (GPP) and ecosystem respiration (ER) in lakes are temperature, nutrients, and light availability, which are predicted to be affected by climate change. Little is known about how these three factors jointly influence shallow lakes metabolism and metabolic status as net heterotrophic or autotrophic. We conducted a pan-European standardized mesocosm experiment covering a temperature gradi- ent from Sweden to Greece to test the differential temperature sensitivity of GPP and ER at two nutrient levels (mesotrophic or eutrophic) crossed with two water levels (1 m and 2 m) to simulate different light regimes. The findings from our experiment were compared with predictions made according the metabolic theory of ecology (MTE). GPP and ER were significantly higher in eutrophic mesocosms than in mesotrophic ones, and in shallow mesocosms compared to deep ones, while nutrient status and depth did not interact. The estimated temperature gains for ER of ~ 0.62 eV were comparable with those predicted by MTE. Temperature sensitivity for GPP was slightly higher than expected ~ 0.54 eV, but when corrected for daylight length, it was more consistent with predictions from MTE ~ 0.31 eV. The threshold temperature for the switch from autotrophy to heterotrophy was lower under mesotrophic (~ 11 C) than eutrophic conditions (~ 20 C). Therefore, despite a lack of signifi- cant temperature-treatment interactions in driving metabolism, the mesocosm’s nutrient level proved to be cru- cial for how much warming a system can tolerate before it switches from net autotrophy to net heterotrophy. We thank the technical staff at the various experimental sites for their support. We thank Alena S. Gesell, Deniz Özkundakci, Jan-Hendrik Schlei- mer, Silke Schmidt, Torsten Seltmann, and Tom Shatwell for their helpful discussions during the preparation of this manuscript. We thank Anne Mette Poulsen, Adam Wilkins, and Michael Thayne for their valuable edit- ing of the manuscript. We are also grateful to reviewers for their valuable comments on the manuscript. This study was supported by FP-7 REFRESH (Adaptive strategies to Mitigate the Impacts of Climate Change on European Freshwater Ecosystems, Contract No. 244121) and the MARS project (Managing Aquatic ecosystems and water Resources under multi- ple Stress), funded under the 7th EU Framework Programme, Theme 6 (Environment including Climate Change), Contract No. 603378 (http:// www.mars-project.eu), TUBITAK- ÇAYDAG (projects No. 105Y332 and 110Y125), the Middle East Technical University (METU)-BAP program of Turkey. EJ was further supported by AU Centre for Water Technology and A_lÇ was also supported by TUBITAK (project 296 Nos. 105Y332 and 110Y125). We thank the technical staff at the various experimental sites for their support. We thank Alena S. Gesell, Deniz Özkundakci, Jan-Hendrik Schlei- mer, Silke Schmidt, Torsten Seltmann, and Tom Shatwell for their helpful discussions during the preparation of this manuscript. We thank Anne Mette Poulsen, Adam Wilkins, and Michael Thayne for their valuable edit- ing of the manuscript. We are also grateful to reviewers for their valuable comments on the manuscript. This study was supported by FP-7 REFRESH (Adaptive strategies to Mitigate the Impacts of Climate Change on European Freshwater Ecosystems, Contract No. 244121) and the MARS project (Managing Aquatic ecosystems and water Resources under multi- ple Stress), funded under the 7th EU Framework Programme, Theme 6 (Environment including Climate Change), Contract No. 603378 (http:// www.mars-project.eu), TUBITAK- ÇAYDAG (projects No. 105Y332 and 110Y125), the Middle East Technical University (METU)-BAP program of Turkey. EJ was further supported by AU Centre for Water Technology and A_lÇ was also supported by TUBITAK (project 296 Nos. 105Y332 and 110Y125).

Efficient zooplankton grazing is a prerequisite for establishing a cascading food web control over phytoplankton in a lake. We studied if the top-down impact of fish could reach phytoplankton in a lake where the grazing pressure of small-sized zooplankton on filamentous phytoplankton is considered weak. We analysed >30 years of data on plankton, fish catches, hydrochemistry, hydrology, and meteorology from Vortsjarv, a large and shallow eutrophic lake in Estonia with intensive commercial fisheries. The lake’s unregulated water level has been considered the strongest factor affecting the ecosystem through modifying sediment resuspension, internal loading of nutrients, and underwater light conditions and spawning conditions for fish. We found a negative relationship between phytoplankton biomass and pikeperch biomass indicating a potential top-down cascading effect in the food web. Top-down control of phytoplankton by zooplankton was reflected in a negative relationship between phyto- and zooplankton biomasses. A decrease of the individual weight of crustacean zooplankton with increasing biomass of small fish suggested top-down control of zooplankton by planktivorous fish. In contrast, we could not demonstrate a direct linkage between piscivorous fish and small fish. The top-down food web impact of piscivores, however, was manifested at zooplankton level in a positive correlation of pikeperch biomass with the biomass of dominating cladoceran species Bosmina coregoni and the individual weight of copepods. At high biomasses of small fish, ciliate domination over metazooplankton increased and thus enhanced the strength of the microbial food web. According to our results, fishery management measures that increase small plankti- and benthivorous fish biomass have to be avoided as they have a cascading negative effect on the ecosystem health.

With increasing primary productivity, ciliates may become the most important members of the microbial loop and form a central linkage in the transformation of microbial production to upper trophic levels. How metazooplankters, especially copepods, regulate ciliate community structure in shallow eutrophic waters is not completely clear. We carried out mesocosm experiments with different cyclopoid copepod enrichments in a shallow eutrophic lake to examine the responses of ciliate community structure and abundance to changes in cyclopoid copepod biomass and to detect any cascading effects on bacterioplankton and edible phytoplankton. Our results indicate that an increase in copepod zooplankton biomass favours the development of small-sized bacterivorous ciliates. This effect is unleashed by the decline of predaceous ciliate abundance, which would otherwise graze effectively on the small-sized ciliates. The inverse relationship between crustacean zooplankton and large predaceous ciliates is an important feature adjusting not only the structure of the ciliate community but also the energy transfer between meta- and protozooplankton. Still we could not detect any cascading effects on bacterio- or phytoplankton that would be caused by the structural changes in the ciliate community.

We estimated the consumption of planktonic ciliates by fish larvae in the Väinameri Sea (a shallow semi-enclosed bay of the Baltic Sea) and Lake Võrtsjärv (a shallow and eutrophic lake). Our primary hypothesis was that planktonic ciliates constitute a substantial component of the diet of fish larvae in both environments. We also assumed that the contribution of ciliates to larval nutrition is bigger in lacustrine than in marine environment because ciliates are usually more abundant in lakes. The nutrition of field collected larval fish was determined by gut content analysis using epifluorescence microscopy. Our study revealed that ciliates occurred in the alimentary tracts of all fish species examined. We discovered that the consumption of ciliates by first-feeding fish larvae contributed approximately 40 and 60% of their total consumed carbon in the Väinameri and in Võrtsjärv, respectively. Ciliates represent essentially important food for fish larvae and sufficient protozoan food may enhance larval growth in the beginning of the exogenous feeding and shorten the most vulnerable period in larval stage before shifting to larger prey. This work was subsidised by institutional research funding IUT 21-02 of the Estonian Ministry of Education and Research, Estonian Science Foundation grants (8511, 8969, 9102) and Swiss Grant for Programme “Enhancing public environmental monitoring capacities”. This work was subsidised by institutional research funding IUT 21-02 of the Estonian Ministry of Education and Research, Estonian Science Foundation grants (8511, 8969, 9102) and Swiss Grant for Programme “Enhancing public environmental monitoring capacities”.

We analysed changes in the abundance, biomass and cell size of the microbial food web community (bacteria, heterotrophicnanoflagellates, ciliates) at contrasting nutrient concentrations and temperatures during a simulated heat wave. We used 24mesocosms mimicking shallow lakes in which two nutrient levels (unenriched and enriched by adding nitrogen and phosphorus)and three different temperature scenarios (ambient, IPCC A2 scenario and A2+%50) are simulated (4 replicates of each).Experiments using the mesocosms have been running un-interrupted since 2003. A 1-month heat wave was imitated by anextra 5◦C increase in the previously heated mesocosms (from 1st July to 1st August 2014). Changes in water temperatureinduced within a few days a strong effect on the microbial food web functioning, demonstrating a quick response of microbialcommunities to the changes in environment, due to their short generation times. Warming and nutrients showed synergisticeffects. Microbial assemblages of heterotrophic nanoflagellates and ciliates responded positively to the heating, the increasebeing largest in the enriched mesocosms. The results indicate that warming and nutrients in combination can set off complexinteractions in the microbial food web functioning. This work was supported by MARS project (ManagingAquatic ecosystems and water Resources under multipleStress, EU 7th Framework Programme, contract no.: 603378)and by institutional grant IUT 21-2 of the Estonian Min-istry of Education and Research. The Danish group wasalso supported by PROGNOS (Predicting in-lake RespOnsesto chanGe using Near real time mOdelS – Water JointProgramme Initiative) and AQUACOSM (Network of Lead-ing European AQUAtic MesoCOSM Facilities ConnectingMountains to Oceans from the Arctic to the Mediterranean),the latter also supporting the Turkish group. Yu Cao issupported by NSF-China (31500296) and CSC (The ChinaScholarship Council). This work was supported by MARS project (ManagingAquatic ecosystems and water Resources under multipleStress, EU 7th Framework Programme, contract no.: 603378)and by institutional grant IUT 21-2 of the Estonian Min-istry of Education and Research. The Danish group wasalso supported by PROGNOS (Predicting in-lake RespOnsesto chanGe using Near real time mOdelS – Water JointProgramme Initiative) and AQUACOSM (Network of Lead-ing European AQUAtic MesoCOSM Facilities ConnectingMountains to Oceans from the Arctic to the Mediterranean),the latter also supporting the Turkish group. Yu Cao issupported by NSF-China (31500296) and CSC (The ChinaScholarship Council).

Lentic ecosystems act as sentinels of climate change, and evidence exists that their sensitivity to warming varies along a latitudinal gradient. We assessed the effects of nutrient and water level variability on zooplankton community composition, taxonomic diversity and size structure in different climate zones by running a standardised controlled 6-months (May to November) experiment in six countries along a European north-south latitudinal temperature gradient. The mesocosms were established with two different depths and nutrient levels. We took monthly zooplankton samples during the study period and pooled a subsample from each sampling to obtain one composite sample per mesocosm. We found a significant effect of temperature on the community composition and size structure of the zooplankton, whereas no effects of water depth or nutrient availability could be traced. The normalised size spectrum became flatter with increasing temperature reflecting higher zooplankton size diversity due to higher abundance of calanoid copepods, but did not differ among depths or nutrient levels. Large-bodied cladocerans such as Daphnia decreased with temperature. Taxonomic diversity was positively related to size diversity, but neither of the two diversity measures demonstrated a clear pattern along the temperature gradient nor with nutrient and water levels. However, genus richness decreased at the warm side of the temperature gradient. Our experiment generally supports recent empirically based findings that a continuing temperature increase may result in lower genus richness and lower abundance of large-sized zooplankton grazers, the latter likely resulting in reduced control of phytoplankton.

We investigated the influence of macrophyte composition on ciliate community structure in a large, shallow, eutrophic Lake Vortsjarv. We hypothesized that macrophyte composition must have strong influence on the dispersal of ecologically different ciliate groups in a shallow lake and that more diverse macrophyte stands cause also a greater diversity in the ciliate community. In Vortsjarv macrophyte distribution is spatially strongly polarized both in east–west and north–south directions in relation to abiotic factors. Phragmites australis and Myriophyllum spicatum were the most widespread species occurring in most parts of the lake. Correlation of environmental, macrophyte and planktonic ciliate variables confirmed the suggested spatial gradients. More diverse macrophyte stands supported a high species richness and abundance of epiplanktonic community but showed negative influence on the number and abundance of euplanktonic ciliate taxa. Opposite trends were found relative to the abundance of P. australis. Benthic ciliates showed a similar distribution pattern to euplanktonic taxa being most abundant in sites were the Shannon–Weaver index for macrophytes was low. Strong polarizing effect of the lake's vegetation on planktonic ciliate diversity was reflected in correlations of the number of ciliate taxa as well as the numbers of eu- and epiplanktonic taxa with geographic co-ordinates.

The feeding impact of planktivorous fish on microbial organisms is still poorly understood. We followed the seasonal dynamics of the food web in two natural fishponds for two years: one was stocked with planktivorous whitefish while the other had no planktivorous fish. The aim of the study was the simultaneous assessment of the feeding behaviours of planktivorous fish and of bacterivorous meta-/protozooplankters. We hypothesized that in the presence of planktivorous fish there would be fewer metazooplankton, more protozoans and decreased numbers of bacteria. Our results showed that the amount of metazooplankton eaten by the fish was indeed negatively correlated with metazooplankton biomass. The feeding impact of planktivorous fish in shaping the microbial loop was remarkable. The main grazers of bacteria in the fishpond were ciliates, whereas in the pond without fish these were heterotrophic nanoflagellates. In the fishless pond the role of the top predator shifted to the predaceous metazooplankter Leptodora kindtii which controlled the abundance of herbivorous metazooplankters. We found a negative relationship between the number of bacteria and flagellates in the fishless pond, while the number of bacterivorous ciliates was suppressed by predaceous ciliates. Therefore the bacteria-grazing activity was higher in the absence of planktivorous fish.

Summary Biogenic methane as an alternative carbon and energy source for freshwater organisms has been receiving increasing attention, but the phenomenon is still poorly understood for shallow lakes. We measured the carbon and nitrogen stable isotope signatures (δ13C, δ15N) for key groups of pelagic and benthic organisms, including crustacean zooplankton, chironomid larvae, young-of-the-year and adult fish, to assess whether biogenic methane contributes to pelagic and benthic food webs in a large, shallow lake, Lake Vortsjarv, Estonia. In the southern part of the lake, covered by macrophytes, crustacean zooplankton showed strong seasonal variation of δ13C, with the lowest values occurring in the period of oxygen depletion. Chironomid (Chironomus plumosus) larvae showed high isotopic variability within the lake, with strongly 13C-depleted and 15N-depleted signatures (down to δ13C −64.0‰ and δ15N −2.6‰) in the macrophyte-covered area. Our results indicate that carbon derived from biogenic methane can contribute seasonally to the benthic food web and, to some extent, also to the pelagic food web, where the lake is covered by macrophytes. Moreover, δ13C values for roach (Rutilus rutilus), perch (Perca fluviatilis) and pike (Esox lucius) from the macrophyte-dominated area were on average 3.5‰ lower than those for the same fish from the plankton-dominated lake area, suggesting some carbon derived from methane is transferred up through the food web. Although no direct evidence is available, our results, together with previous studies of the lake, suggest that protozoans could be a potentially important link from methane-oxidising bacteria to animals higher in the web.

Summary 1. As grazers on picoplankton and nanoplankton, planktonic ciliates form an important link in pelagic food webs. Ciliate communities may be controlled by predation by metazooplankton. In eutrophic systems, however, where the number of large crustaceans is often low, the mechanisms that regulate ciliate dynamics have rarely been described. 2. We conducted an enclosure experiment with natural and screened (145 μm) summer plankton communities to investigate the effect of the small-sized crustacean zooplankton on ciliate community structure and the microbial loop in a shallow eutrophic lake. 3. The removal of the larger fraction of crustaceans initiated a decrease in total ciliate abundance. At the community level, we observed a substantial increase in large-sized predacious ciliates (>100 μm) and a simultaneous decrease in the abundance of smaller ciliates (

We assessed feeding of planktivorous fish larvae on ciliate protozooplankton in shallow eutrophic Lake Vortsjarv, Estonia to determine whether ciliates are an important part of larval fish diet. We collected larvae of the most common fish species and examined their gut contents by gut segmentation and epifluorescence microscopy. Ciliates were present in the gut of all fish larvae. Gut segmentation analysis showed clear differences in food composition between gut quarters. The hard-bodied food items were quite evenly distributed in the gut, but the soft-bodied ciliates and rotifers were present only in the first gut quarters. Neglecting differences in prey digestion rate leads to underestimation of diet amount and composition and, especially, to underestimation of the role of protists in food. In Vortsjarv, ciliates account for ∼ 60% of the total carbon biomass consumed by fish larvae. The food requirement of fish larvae during first feeding stages (May-Jun) would not be met without consumption of ciliates.

Seasonal population dynamics and community composition of planktonic ciliates were studied for over a decade in a naturally eutrophic shallow lake, Lake Vortsjarv, which has a large open surface area (270 km 2 on average) and highly turbid water (Secchi depth 300 µm) gymnostomes. There was a positive correlation between ciliates and phyto- and bacterioplankton, implying that the ciliates were clearly bottom-up or food-controlled. This was further confi rmed by the positive correlation between ciliates and metazooplankton. As both bacteria and phytoplankton are coupled with resuspension of lake sediments, the large fl uctuations in water level infl uenced the ciliate community biomass annually.

The aim of the present study was to describe the role of ciliates and heterotrophic nanoflagellates in macrophyte and phytoplankton dominated shallow lakes and to compare the grazing on pico- and nano-sized particles by these protozoans. We sampled three shallow lakes, seasonally, one dominated by macrophytes, one by phytoplankton, and one with both conditions (two basins of this lake were sampled separately). The role of ciliates as consumers of bacteria and small algae was important in both lake types. In plankton dominated lakes the grazing rate of ciliates on bacteria was higher than in macrophyte dominated ones. But when ciliates were grazing on small algae, the highest rates were found in macrophyte lakes. Our results suggest that the microbial loop is weaker in macrophyte dominated lakes and grows stronger, when a lake becomes more turbid. The dominance of herbivorous ciliates in macrophyte lakes in summer and their high grazing rates on phytoplankton may have contributed to the decrease in phytoplankton abundance in these lakes. Heterotrophic nanoflagellates were relatively less abundant and, due to their low specific filtering rates, grazed only a minor fraction of the bacterioplankton.

The abundance and biomass of ciliates, rotifers, cladocerans and copepods were studied in Lake Peipsi and Lake Vortsjarv, both of which are shallow, turbid and large. Our hypothesis was that in a large shallow eutrophic lake, the ciliates could be the most important zooplankton group. The mean metazooplankton biomass was higher in Peipsi than in Vortsjarv (mean values and SD, 1.8 ± 0.7 and 1.3 ± 0.6 mg WM l−1). In Peipsi, the metazooplankton biomass was dominated by filtrators that feed on large-sized phytoplankton and are characteristic of oligo-mesotrophic waters. In Vortsjarv, the metazooplankton was dominated by species characteristic of eutrophic waters. The planktonic ciliates in both lakes were dominated by oligotrichs. The biomass of ciliates was much greater in Vortsjarv (mean 2.3 ± 1.4 mg WM l−1) than in Peipsi (0.1 ± 0.08 mg WM l−1). Ciliates formed about 60% of the total zooplankton biomass in Vortsjarv but only 6% in Peipsi. Thus, the food chains in the two lakes differ: a grazing food chain in Peipsi and a detrital food-chain in Vortsjarv. Consequently, top-down control of phytoplankton can be assumed to be much more important in Peipsi than in Vortsjarv. When the detrital food chain prevails, the planktonic ciliates become the most important zooplankton group in shallow, eutrophic and large lake. Neglecting protozooplankton can result in serious underestimates of total zooplankton biomass since two-thirds of the zooplankton biomass in Vortsjarv comprises ciliates.

The grazing impact of different sized zooplankton on ‘edible’ and total phytoplankton biomass and primary production was measured in L. Vortsjarv during a seasonal study in 1998 and 2000. The organisms of 48–100 μm size class, composed of ciliates and rotifers, contributed significantly to the total grazing of zooplankton community throughout the study period (average 68%). The average daily filtering and grazing rate of the whole zooplankton community (micro- and macro-zooplankton) remained low, corresponding to a filtration of 44% of the water volume, 4% of the total phytoplankton biomass and 29% of primary production. However, a strong grazing pressure on small-sized phytoplankton (

Periphyton communities play an important role in shallow lakes and are controlled by direct forces such as temperature, light, nutrients, and invertebrate grazing, but also indirectly by planktivorous fish predation. We performed a pan-European lake mesocosm experiment on periphyton colonization covering five countries along a north/south geographical/temperature gradient (Estonia, Germany, Czech Republic, Turkey, and Greece). Periphyton biomass on artificial polypropylene strips exposed at 50 cm water depth at low and high nutrient regimes (with mean total phosphorus concentration of 20 and 65 mu g L-1, respectively) was compared during mid-summer. No significant effect of nutrient loading on periphyton biomass was observed as nutrient concentrations in the mesocosms were generally above limiting values. Water temperature significantly enhanced summer periphyton biomass development. Additionally, direct and indirect top-down control of snails and fish emerged as a significant factor in periphyton biomass control.

Quick changes in community composition and population dynamics of planktonic ciliates were studied in the ponds of two fish farms obtaining water from different sources (from a fast flowing river or a stillwater reservoir). Samples were taken at two-day intervals during a short period after springtime filling of the ponds. At the beginning of the investigation period the community in the lotic ponds was dominated by species that favour periphyton or benthos as their habitat. They were gradually replaced by euplanktonic species. In the lentic ponds euplanktonic species dominated throughout our study. The similarity index ISj between lotic ponds and their inflow was 0.67 at the start of our study but decreased to 0.2 during 14 days. If the inflow was from a stillwater reservoir, the similarity index decreased only moderately. In the lotic ponds ciliate community shifted from bacterivory to algivory while in the case of lentic ponds the situation was the opposite - algivorous species were gradually replaced by bacterivores. Abiotic and biotic factors that determine ciliate community structure were separated. The abiotic features are ruling when the system goes through major changes (in our study the lotic pond system where water flow ceased dramatically). The biotic factors are crucial in more stable systems (in our study the lentic pond system) and can change the community structure in same degree as the abiotic ones.

Climate change is expected to profoundly affect both temperature and net precipitation, with implications for lake water level. We describe the design of a harmonized, simultaneous, cross- European mesocosm experiment to elucidate the effects of climate change on community structure, functioning, and metabolism in shallow lakes at low and high nutrient levels with contrasting depths (1 and 2 m). We used cylindrical (D = 1.2 m) tanks that were either 1.2 or 2.2 m high, each having a 10-cm sediment layer. We inoculated the mesocosms with a mixed sample of sediment and plankton from lakes with contrasting nutrient concentrations and added macrophytes and planktivorous fish. Sediment was pre-equilibrated to the required experimental nutrient concentration. During the experiment the water level decreased with increasing temperature (up to 90 cm in the Mediterranean mesocosms) while conductivity increased. The average chlorophyll a concentration increased with temperature in the deep mesocosms but was more variable in the shallow mesocosms. Macrophyte

The influence of functional group specific production and respiration patterns on a lake's metabolic balance remains poorly investigated to date compared to whole-system estimates of metabolism. We employed a summed component ecosystem approach for assessing lake-wide and functional group-specific metabolism (gross primary production (GPP) and respiration (R)) in shallow and eutrophic Lake Vortsjarv in central Estonia during three years. Eleven functional groups were considered: piscivorous and benthivorous fish; phyto-, bacterio-, proto- and metazooplankton; benthic macroinvertebrates, bacteria and ciliates; macrophytes and their associated epiphytes. Metabolism of these groups was assessed by allometric equations coupled with daily records of temperature and hydrology of the lake and measurements of food web functional groups biomass. Results revealed that heterotrophy dominated most of the year, with a short autotrophic period observed in late spring. Most of the metabolism of the lake could be attributed to planktonic functional groups, with phytoplankton contributing the highest share (90% of GPP and 43% of R). A surge of protozooplankton and bacterioplankton populations forming the microbial loop caused the shift from auto- to heterotrophy in midsummer. Conversely, the benthic functional groups had overall a very small contribution to lake metabolism. We validated our ecosystem approach by comparing the GPP and R with those calculated from O2 measurements in the lake. Our findings are also in line with earlier productivity studies made with 14C or chlorophyll a (chl-a) based equations. Ideally, the ecosystem approach should be combined with diel O2 approach for investigating critical periods of metabolism shifts caused by dynamics in food-web processes.

The objective of this study was to investigate the relationships between bacterioplank- ton biomass and activity and protistan grazing during the spring in shallow Lake Vortsjarv, Estonia. Bacterial and heterotrophic protistan (flagellate and ciliate) abundance was determined by fluores- cence direct counts, protistan grazing on planktonic bacteria was measured from fluorescently labeled bacteria uptake rates, and the estimate of bacterial heterotrophic activity was obtained from leucine and thymidine incorporation rates. The abundance of heterotrophic nanoflagellates (HNF) was low, ranging from 8.4 to 27.1 cells ml -1 , while ciliate numbers dominated, ranging from 55 to 180 cells ml -1 . The population of ciliated protozoans was dominated by scuticociliates (Uronema sp., Cyclidium spp., and 1 unidentified scuticociliate) and oligotrichs (Strobilidium spp. (diameter > 50 µm), Strobilidium spp. (diameter < 50 µm), and Strombidium sp.). Ciliates were predominant grazers of bacteria, showing higher clearance rates (14 to 65 nl ciliate -1 h -1 ) than HNF (1 to 11 nl HNF -1 h -1 ); the total grazing rate of ciliates (on average 2398 bacteria h -1 ml -1 ) was 28 times higher than total graz- ing of HNF (87 bacteria h -1 ml -1 ). In general terms protozoan grazing balanced with bacterial pro- duction but was not sufficient to support ciliate growth: on the basis of conversion factors the calcu- lated generation time of bacterivorous ciliates was long, on average 121 d (ranging from 43 to 198 d).

The vertical distribution of planktonic ciliates in eight strongly stratified temperate lakes was studied in summer 1998. Ciliate abundance and biomass were highest (mean 39.9 cells ml−1 and 181.9 μg C l−1) in the epi-, and lowest (mean 8.2 cells ml−1 and 97.6 μg C l−1) in the hypolimnion. The community of ciliates was dominated by five orders: Oligotrichida, Haptorida, Prostomatida, Scuticociliatida and Peritrichida. The community composition varied greatly with depth. In the epilimnion, the ciliate numbers were dominated by oligotrichs but small algivorous prostomatids, peritrichs and haptorids were also numerous. In the metalimnion, these groups were replaced by scuticociliates and mixotrophic prostomatids. In the hypolimnion species known as benthic migrants appeared. We found a positive significant correlation (p < 0.05) between ciliate numbers and Chl a and bacterial densities. Only in the hypolimnion, the correlation between ciliates numbers and Chl a was not significant.

An analysis of plankton seasonal succession in large shallow eutrophic lake Vortsjarv (270 km 2 , mean depth 2.8 m, max. depth 6 m) is presented. Weekly samples for 1995 have been analysed using the PEG model approach. In winter, light was the main factor controlling phytoplankton growth. In early spring phytoplankton was mainly resource-controlled, competition for phosphorus being the main driving force. Ciliates (Paradileptus sp., Strobilidium sp. and Vorticella sp.) were the first herbivores which started to increase in April causing a twofold decline of phytoplankton biomass. The annual maximum of primary production (PP) in early May was probably caused by soluble reactive phosphorus (SRP), regenerated by herbivores, and stirred up from bottom sediments as a result of strong wind stress. This primary production peak provided substrate for further increase of bacterial biomass. The more abundant food supply supported the development of the second spring peak of herbivores (ciliates, rotifers, juvenile copepods) which was followed by the second modest clear water phase in late May. Silicon was depleted by the end of May causing a strong decrease in primary production of the diatom-dominated community. whereas the biomass of the cyanophytes increased under the improved nutrient conditions. Some weeks later, inorganic N was depleted and the period of N limitation with the appearance of N-fixing cyanophytes began. The ciliate collapse at the beginning of June coincided with the start of the cladoceran development and with the increase of other metazooplankton groups. This explains the further decrcase of the biomass of phytoplankton and bacteria in spite of their high production. Beginning from late June, silicon appeared again and SRP started to occur periodically. while inorganic N remained close to zero until November. During this period, phytoplankton development relied to a great extent on the N-fixation and N-regeneration potential. The collapse of the ciliate community in September removed the top-down control from bacteria and their biomass increased, while the development of cladocerans still suppressed phytoplankton biomass in spite of a quite high PP. In October phytoplankton biomass and chlorophyll a (Chla) increased, SRP was completely depleted by the middle of October reflecting a slow regeneration due to the declined activity of zooplankton in cold water. In November nitrates appeared again. and silicon reached the same level as in spring. The biomass of N-fixing Aphanizomenon skujae decreased while Limnothrix redekei and L. planctonica were quite abundant together with diatoms.

The diel dynamics of bacterio- and phytoplankton as main compartments in the pelagic foodweb were followed in order to assess the coupling between algal photosynthesis and bacterial growth during a diel cycle in Lake Vorstjarv, Estonia. Three diurnal studies were carried out, on July 12th–13th, 1994; on June 25th–26th, 1995 and on July 17th–18th, 1995 with a sampling interval of 3–4 hours. Diel variations in bacterial number, biomass and productivity, in phytoplankton primary production and extracellular release of photosynthetic products, in ciliate number and biomass were followed. Phytoplankton was dominated by filamentous species: Limnothrix redekei, Oscillatoria sp., Aulacoseira (Melosira) ambigua and Planktolyngbya limnetica. The abundance of bacteria ranged from 4.1 to 14.6 · 1012 cells m-2 (median 9.88). The production of heterotrophic bacteria varied from 0.6 to 11 mgC m-2 h-1 (median 3.65), the variation during diel cycle was high. Depth integrated values of particulate (PPpart) and extracellular primary production (PPdiss) ranged from 6 to 55 and from 17 to 90 mgC m- 2 h-1, respectively. About 50 ciliate taxa were identified among them more abundant were bacterivores, bacterivores- herbivores and omnivores. Biomass of bacterivorous ciliates (TCbact) varied from 8 to 427 mgC m-2. Bacterioplankton production constituted not more than 20% of total primary production (particulate + released), dynamics of bacterial production was related to the primary production, the correlation was negative with PPpart and positive with PPdiss. Different types of potential controlling factors of bacterioplankton (N and P nutrient control, bottom-up control by food and top-down control) are discussed.

Abundance and biomass of the microbial loop members [bacteria, heterotrophic nanoflagellates (HNF), and ciliates] were seasonally measured in the naturally eutrophic and shallow (2.8 mean depth) Lake Võrtsjärv, which has a large open surface area (average 270 km2) and highly turbid water (Secchi depth1 m). Grazing rates (filter feeding rates) on 0.5-, 3-, and 6-microm-diameter particles were measured to estimate pico- and nanoplankton grazing (filter feeding) by micro- and metazooplankton. Among grazers, HNF had a low abundance (50 cells mL-1) and, due to their low specific filtering rates, they only grazed a minor fraction of the bacterioplankton (or=4.2% of total grazing). Ciliates were relatively abundant (or=158 cells mL-1) and, considering their high specific feeding rates, were able to graze more than 100% of the bacterial biomass production in the open part of the lake, whereas the average daily grazing accounted for 9.3% of the bacterial standing stock. Ciliates were potentially important grazers of nanoplanktonic organisms (on average, approximately 20% of the standing stock of 3-microm-size particles was grazed daily). Metazooplankton grazed a minor part of the bacterioplankton, accounting for only 0.1% of standing stock of bacteria. Grazing on nanoplankton (3-6 microm) by metazooplankton was higher (0.4% of standing stock). The hypothesis is proposed that ciliates dominate due to a lack of top-down regulation by predators, and HNF have a low abundance due to strong grazing pressure by ciliates.

Seasonal population dynamics and the vertical distribution of planktonic ciliates in a hypertrophic and strongly stratified temperate lake were studied from April to October in 2000 and from April to June in 2001. In the epi- and metalimnion the ciliate abundance peaked in spring and late summer, reaching maximum values in the metalimnion (86 cells ml−1) on 7th August 2000. In the epilimnion, the highest biomass content (414 µg C l−1) was observed on 8th May 2000. In the hypolimnion only a late summer peak occurred and the ciliate numbers were always lower than in the epi- and metalimnion. Five groups dominated the community of ciliates: Oligotrichida, Gymnostomatea, Prostomatida, Hymenostomata and Peritrichia, and the community composition varied greatly with depth. In the epilimnion the ciliate numbers were dominated by oligotrichs but small algivorous prostomatids, peritrichs and gymnostomes were also numerous. In the metalimnion these groups were gradually replaced by scuticociliates and mixotrophic Coleps spp. In the hypolimnion scuticociliates and species known as benthic migrants dominated. In the epilimnion and upper metalimnion in spring large herbivores and in summer small bacterivores were more numerous.

The wastewaters of an iron mining company in NW Russia have changed the water quality in some forest lakes to be hard with a high pH, in contrast to the soft water and low pH in natural lakes. Two impacted lakes and a reference lake were sampled once in early August in three successive years for water quality, plankton communities, and fish. The concentrations of potassium, lithium, and sulphate were high in the impacted lakes. Total phosphorus was low (~ 10 µg L -1 ) in all lakes. The primary producers' biomass and chlorophyll a content in the impacted lakes were high because of high densities of autotrophic picocyanobacteria (Synechococcus spp.). All planktonic communities showed a changed taxa composition and lower species richness. Zooplankton was predominantly Rotatoria in all the lakes. In the impacted lakes, Cladocera was represented by Bosmina, and Copepoda by small cyclopoids. The most obvious substance to be harmful to some planktonic species was potassium. The high pH and high mineral content of the water obviously lower both the toxicity and the bioavailability of heavy metals in the impacted lakes.

We studied the relationships between the planktonic food base and feeding patterns of juvenile mid-summer/ early autumn Eurasian perch Perca fluviatilis L., a common predatory freshwater fish in large parts of Europe and Asia. The feeding of 0+ perch was studied during summer and autumn in littoral habitats of seven lakes with different environmental conditions –four Latvian (Auciema, Riebinu, Vārzgūnes, Laukezers) and three Estonian (Kaiavere, Prossa and Akste) lakes. Simultaneously, the abundance, biomass and structure of zooplankton communities were examined. We focused on the littoral areas because many studies in lakes suggest that littoral habitats are particularly important for 0+ fish growth and survival. We were interested in the question: can the diet and growth of 0+ perch be explained by zooplankton community structure? We also presumed that if the amount of zooplankton is low, more benthic invertebrates will be consumed by 0+ perch. Opposite to expectations, we found that zooplankton always counted for over 90% of diet biomass in perch. There were also clear correlations between the zooplankton biomass in a given lake, the zooplankton biomass in 0+ perch stomachs, and the fish growth rate. The study also suggested that nutrient enrichment can positively impact the 0+ perch feeding conditions in lakes. The project is financed by the European Regional Development Fund, the State budget of the Republic of Latvia and the foundation “Institute for Environmental Solutions”. Funding for this project was also provided by the European Union‘s Horizon 2020 research and innovation programme under Grant Agreement No. 951963 (TREICLAKE “Towards Research Excellence and Innovation Capacity in Studying Lake Ecosystems Functional Structures and Climate Change Impact”). The project is financed by the European Regional Development Fund, the State budget of the Republic of Latvia and the foundation “Institute for Environmental Solutions”. Funding for this project was also provided by the European Union‘s Horizon 2020 research and innovation programme under Grant Agreement No. 951963 (TREICLAKE “Towards Research Excellence and Innovation Capacity in Studying Lake Ecosystems Functional Structures and Climate Change Impact”).

We modeled energy transfer and trophic position of fish, plankton, and macroinvertebrates and the relative importance of top-down versus bottom-up processes in Lake Võrtsjärv, a large shallow eutrophic lake in Estonia (northeastern Europe). We employed input values based on 37 years of biomass and fishing activity monitoring for calibrating the Ecopath with Ecosim (EwE) model. Energy flows from primary producers and detritus, represented by total system throughput, were nearly equal (51 and 49%, respec- tively). Simulation revealed that top-down and bot- tom-up forces were at play, metazooplankton was not efficiently grazing phytoplankton production, and a trophic cascade proceeded through macroinverte- brates rather than through zooplankton. Detritivory was responsible for the relatively low trophic position of Võrtsjärv fish compared to other lakes. Bottom-up processes were the main drivers for the dual, primary production- and detritus-based pathways in energy flow. Our findings suggest that the predicted biomass increase of cyanobacteria in shallow lakes in the future will strengthen the reliance of consumers on the detrital pathway at the expense of the primary production pathway. This research was supported by the Start-Up Personal Research Grant PUT 777 to FC and UB, by IUT 21-2 of the Estonian Ministry of Education and Research, and by MARS project (Managing Aquatic ecosystems and water Resources under multiple Stress) funded under the 7th EU Framework Programme, Theme 6 (Environment including Climate Change), Contract No.: 603378 (http://www.mars-project.eu). This research was supported by the Start-Up Personal Research Grant PUT 777 to FC and UB, by IUT 21-2 of the Estonian Ministry of Education and Research, and by MARS project (Managing Aquatic ecosystems and water Resources under multiple Stress) funded under the 7th EU Framework Programme, Theme 6 (Environment including Climate Change), Contract No.: 603378 (http://www.mars-project.eu).

Seasonal population dynamics and community composition of planktonic ciliates of shallow eutrophic Lake Vortsjarv were studied from January 1995 to December 1996. The abundances (1995 mean = 39.0 × 10 3 cells/l, 1996 mean = 60.1×10 3 cells/l) and biomasses (1995 mean = 0.68 mg/l, 1996 mean = 2.91 mg/l) were high and showed an increasing trend with the decrease in water level. Ciliate abundances peaked in spring (May) and in late summer (July, August) reaching values up to 191.1 × 10 3 cells/l. The biomass maxima did not coincide with maximum abundances and were tied with the mass occurrences of large-sized carnivorous species. Ciliates accounted for 50 to 64 % of the zooplankton biomass (in 1995 and 1996, respectively). Oligotrichs, haptorids, scuticociliates and prostomatids dominated the community of ciliates.

Aquatic macrophyte taxonomic composition, species abundance and cover determine the physical structure, complexity and heterogeneity of aquatic habitats – the structuring role of macrophytes. These traits influence richness, distribution, feeding and strength of the relationships between food web communities in lakes. The aim of this study was to determine how lakes with different dominating macrophyte ecological groups affect planktonic food web components, emphasising the influence on young of year (YOY) fish and large (≥1 +) fish community. We hypothesised that different dominating macrophyte ecological groups have different structural effects on food web components and YOY fish growth, abundance and feeding. Studied lakes categorised into three different macrophyte ecological groups – lakes dominated by emergent, floating+floating-leaved or submerged vegetation. We found that all dominating ecological groups had a strong influence on plankton communities (except heterotrophic bacterioplankton and nanoflagellates), YOY fish and large fish. Floating-leaved plant dominance was positively related to planktonic food web structure and YOY fish weight, length, abundance and the consumption of zooplankton as a prey of all major species of YOY fishes. Larger fish tended to favour the presence of emergent vegetation. This conclusion has important implications for local managers and conservationists in respect to the maintenance and protection of littoral habitats and fish resources. The project is financed by the European Regional Development Fund, the State budget of the Republic of Latvia and the foundation “Institute for Environmental Solutions”. Also, this project has received funding from the European Union‘s Horizon 2020 research and innovation programme under Grant Agreement No. 951963. The project is financed by the European Regional Development Fund, the State budget of the Republic of Latvia and the foundation “Institute for Environmental Solutions”. Also, this project has received funding from the European Union‘s Horizon 2020 research and innovation programme under Grant Agreement No. 951963.