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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.

The study of lake sediments and archived biological remains is a promising approach to better under- stand the impacts of climate change on aquatic ecosystems. Small lakes have been shown to be strongly sensitive to past climate change, but similar information is lacking for large lakes. By identifying re- sponses to climate change of carbon flows through benthic food web in two different sized lakes, we aimed to understand how lake morphometry can mediate the effects of climate change. We recon- structed the dynamics of phytoplankton community composition and carbon resources sustaining chironomid biomass during the Holocene from the combined analysis of sedimentary pigment quanti- fication and carbon stable isotopic composition of subfossil chironomid head capsules (d13 C HC) in a large lake in the Baltic area (Estonia). Our results showed that chironomid biomass in the large lake was mainly sustained by phytoplankton, with no significant relationship between d13 C HC values and tem- perature fluctuations. We suggest that lake morphometry (including distance of the sampling zone to the shoreline, and lake volume for primary producers) mediates the effects of climate change, making large lakes less sensitive to climate change. Complementary studies are needed to better understand differ- ences in organic matter dynamics in different sized lakes and to characterize the response of the aquatic carbon cycle to past climate change. Financial support was provided by institutional research grants IUT1-8 and IUT21-2 from the Estonian Science Agency and by Estonian University of Life Sciences, project No. 8M160101PKLJ. We are grateful to Christian Hossann (INRA Nancy, Champenoux) for assistance in carbon stable isotope analysis. The PTEF facility is supported by the French National Research Agency through the Laboratory of Excellence ARBRE (ANR-11-LABX-0002-01). We acknowledge the contributions of Atko Heinsalu, Siim Veski and Jüri Vassiljev for coring and sediment dating. We also thank G. L. Simpson for valuable comments on statistical analyses. Editing services were provided by Sea Pen Scientific Writing. Financial support was provided by institutional research grants IUT1-8 and IUT21-2 from the Estonian Science Agency and by Estonian University of Life Sciences, project No. 8M160101PKLJ. We are grateful to Christian Hossann (INRA Nancy, Champenoux) for assistance in carbon stable isotope analysis. The PTEF facility is supported by the French National Research Agency through the Laboratory of Excellence ARBRE (ANR-11-LABX-0002-01). We acknowledge the contributions of Atko Heinsalu, Siim Veski and Jüri Vassiljev for coring and sediment dating. We also thank G. L. Simpson for valuable comments on statistical analyses. Editing services were provided by Sea Pen Scientific Writing.

The benthic foodweb structure of Lake Võrtsjärv, a large (270 km2), shallow, and turbid Estonian lake, was evaluated based on C and N stable-isotope signatures (δ13C, δ15N). Variation in δ13C between sampling sites was not related to site proximity to the littoral zone or the more vegetated southern part of the lake, but rather appeared to be influenced by in-situ site peculiarities. δ13C was stable temporally and between functional feeding groups, a result implying that the whole benthic food web of the lake relies largely on the same C source admixture, essentially particulate organic matter (POM). Thus, the foodweb composition of Lake Võrtsjärv is remarkably homogeneous given the lake’s large surface area. Apparent trophic-level δ15N fractionation between total collectors and total predators (mean 1.7‰) was lower than the value of 3.4‰ generally adopted in foodweb studies, but the higher value was valid for specific prey–predator links. The low δ13C signature of some chironomid samples indicated probable assimilation of methane-oxidizing bacteria (MOB) by these sediment-dwelling invertebrates. However, the lack of similar 13C depletion in benthic filterers (mussels) indicated that the MOB layer is essentially confined to the sediments and does not reach the water column, which probably constrains transfer of methane-derived C through the food web to fish in this lake. Our study demonstrates that the benthic food web of shallow turbid lakes like Võrtsjärv is simplified and is mostly sustained by phytoplanktonic C sources. peerReviewed

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.

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).

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.