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Lakes are considered important regulators of atmospheric greenhouse gases (GHG). We estimated late summer open water GHG fluxes in nine hemiboreal lakes in Estonia classified under different lake types according to the European Water Framework Directive (WFD). We also used the WFD typology to provide an improved estimate of the total GHG emission from all Estonian lakes with a gross surface area of 2204 km2 representing 45,227 km2 of hemiboreal landscapes (the territory of Estonia). The results demonstrate largely variable CO2 fluxes among the lake types with most active emissions from Alkalitrophic (Alk), Stratified Alkalitrophic (StratAlk), Dark Soft and with predominant binding in Coastal, Very Large, and Light Soft lakes. The CO2 fluxes correlated strongly with dissolved CO2 saturation (DCO2) values at the surface. Highest CH4 emissions were measured from the Coastal lake type, followed by Light Soft, StratAlk, and Alk types; Coastal, Light Soft, and StratAlk were emitting CH4 partly as bubbles. The only emitter of N2O was the Alk type. We measured weak binding of N2O in Dark Soft and Coastal lakes, while in all other studied lake types, the N2O fluxes were too small to be quantified. Diversely from the common viewpoint of lakes as net sources of both CO2 and CH4, it turns out from our results that at least in late summer, Estonian lakes are net sinks of both CO2 alone and the sum of CO2 and CH4. This is mainly caused by the predominant CO2 sink function of Lake Peipsi forming ¾ of the total lake area and showing negative net emissions even after considering the Global Warming Potential (GWP) of other GHGs. Still, by converting CH4 data into CO2 equivalents, the combined emission of all Estonian lakes (8 T C day−1 ) is turned strongly positive: 2720 T CO2 equivalents per day. This research was inspired by GLEON (Global Lake Ecological Observatory Network) and was funded by Estonian Research Council (PSG32, PUT1598, PSG10, PRG709, PRG1167 and ETF8486), the European Union H2020 WIDESPREAD (TREICLAKE 951963) and the Swiss Program “Enhancing public environmental monitoring capacities”. This research was inspired by GLEON (Global Lake Ecological Observatory Network) and was funded by Estonian Research Council (PSG32, PUT1598, PSG10, PRG709, PRG1167 and ETF8486), the European Union H2020 WIDESPREAD (TREICLAKE 951963) and the Swiss Program “Enhancing public environmental monitoring capacities”.

The frequency of heatwave events in Europe is increasing as a result of climate change. This can have implications for the water quality and ecological functioning of aquatic systems. We deployed three spectroradiometer WISPstations at three sites in Europe (Italy, Estonia, and Lithuania/Russia) to measure chlorophyll-a at high frequency. A heatwave in July 2019 occurred with record daily maximum temperatures over 40 ◦C in parts of Europe. The effects of the resulting storm that ended the heatwave were more discernable than the heatwave itself. Following the storm, chlorophyll-a concentrations increased markedly in two of the lakes and remained high for the duration of the summer while at one site concentrations increased linearly. Heatwaves and subsequent storms appeared to play an important role in structuring the phenology of the primary producers, with wider implications for lake functioning. Chlorophyll-a peaked in early September, after which a wind event dissipated concentrations until calmer conditions returned. Synoptic coordinated high frequency monitoring needs to be advanced in Europe as part of water management policy and to improve knowledge on the implications of climate change. Lakes, as dynamic ecosystems with fast moving species-succession, provide a prism to observe the scale of future change. This research is part of the H2020 EOMORES (GA n. 730066) and ESA CCI LAKES project (GA n. 40000125030/18/I-NB). We would like to thank the “Cooperativa dei Pescatori del Trasimeno” for the support in the WISPstation installation and maintenance, ARPA Umbria for useful discussions, and the Province of Perugia for the availability to use the platform in Polvese Island. Research in Estonia was also financed by Estonian Research Council grants PSG10 and PUT1598. Centre for Limnology is thanked for the opportunity to use the pier for WISPstation instal- lation and Ilmar Ansko and Martin Ligi for the instrument maintenance. We kindly acknowledge the Lithuanian Hydrometeorological Service under the Ministry of Environment for the provided meteorological data. We would like to thank the Curonian Spit National Park and Administration of Neringa municipality for the permission to install the WISPstation in Pervalka (the Curonian Lagoon, Lithuania) and Vilius Zeigis and Jonas Gintauskas for the instrument installation and maintenance. We thank Daniela Stroppiana for help with the analysis of the water spectral signatures. We thank the editor and three reviewers for their time in providing comments and suggestions that improved this manuscript. This research is part of the H2020 EOMORES (GA n. 730066) and ESA CCI LAKES project (GA n. 40000125030/18/I-NB). We would like to thank the “Cooperativa dei Pescatori del Trasimeno” for the support in the WISPstation installation and maintenance, ARPA Umbria for useful discussions, and the Province of Perugia for the availability to use the platform in Polvese Island. Research in Estonia was also financed by Estonian Research Council grants PSG10 and PUT1598. Centre for Limnology is thanked for the opportunity to use the pier for WISPstation instal- lation and Ilmar Ansko and Martin Ligi for the instrument maintenance. We kindly acknowledge the Lithuanian Hydrometeorological Service under the Ministry of Environment for the provided meteorological data. We would like to thank the Curonian Spit National Park and Administration of Neringa municipality for the permission to install the WISPstation in Pervalka (the Curonian Lagoon, Lithuania) and Vilius Zeigis and Jonas Gintauskas for the instrument installation and maintenance. We thank Daniela Stroppiana for help with the analysis of the water spectral signatures. We thank the editor and three reviewers for their time in providing comments and suggestions that improved this manuscript.

The authors acknowledge COST Action ES 1105 "CYANOCOST Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management" and COST Action Global Change Biology ES 1201 NETLAKE -Networking Lake Observatories in Europe" for contributing to this study through networking and knowledge sharing with European experts in the field. We acknowledge the members of the Global Lake Ecological Observatory Network (GLEON) for their collaborative spirit and enthusiasm that inspired the grassroots effort of the EMLS. E.M. was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation to Bas Ibelings and by supplementary funding from University of Geneva. We thank Wendy Beekman for the nutrient analysis. We thank Pieter Slot for assisting with the pigment analysis. We thank Dr. Ian Jones for valuable feedback on an earlier version of the manuscript. We thank the Leibniz Institute of Freshwater Ecology and the Aquatic Microbial Ecology Group for logistic and technical support of J. Fonvielle and H.-P. Grossart, and the Leibniz Association for financial support. H.P. was supported by the US National Science Foundation (1840715, 1831096). A.C.'s work was funded by the Spanish Agencia Estatal de Investigacion and EU funds through the project CLIMAWET (CGL2015-69557-R). The collection of data for Lough Erne and Lough Neagh were funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland. We are grateful to Kristiina Vuorio from the Freshwater Centre of the Finnish Environment institute for her help in organizing, collecting and analysing samples by the University of Jyvaskyla and to Gerald Dorflinger from the Water Development Department of Cyprus for his assistance with the sampling in Cyprus and for granting the CUT team permission to use WDD's equipment. Finally, we would like to thank the numerous other assistants that helped realizing each local survey. Open access funding provided by Universite de Geneve., To determine the drivers of phytoplankton biomass, we collected standardized morphometric, physical, and biological data in 230 lakes across the Mediterranean, Continental, and Boreal climatic zones of the European continent. Multilinear regression models tested on this snapshot of mostly eutrophic lakes (median total phosphorus [TP] = 0.06 and total nitrogen [TN] = 0.7 mg L-1), and its subsets (2 depth types and 3 climatic zones), show that light climate and stratification strength were the most significant explanatory variables for chlorophyll a (Chl a) variance. TN was a significant predictor for phytoplankton biomass for shallow and continental lakes, while TP never appeared as an explanatory variable, suggesting that under high TP, light, which partially controls stratification strength, becomes limiting for phytoplankton development. Mediterranean lakes were the warmest yet most weakly stratified and had significantly less Chl a than Boreal lakes, where the temperature anomaly from the long-term average, during a summer heatwave was the highest (+4 degrees C) and showed a significant, exponential relationship with stratification strength. This European survey represents a summer snapshot of phytoplankton biomass and its drivers, and lends support that light and stratification metrics, which are both affected by climate change, are better predictors for phytoplankton biomass in nutrient-rich lakes than nutrient concentrations and surface temperature., European Cooperation in Science and Technology (COST) ES 1105 ES 1201, Swiss State Secretariat for Education, Research and Innovation, University of Geneva, Leibniz Association, National Science Foundation (NSF) 1840715 1831096, Spanish Agencia Estatal de Investigacion, European Commission CGL2015-69557-R, Department of Agriculture, Environment and Rural Affairs, Northern Ireland

European countries are obligated to monitor and estimate ecological status of lakes under European Union Water Framework Directive (2000/60/EC) for sustainable lakes’ ecosystems in the future. In large and shallow lakes, physical, chemical, and biological water quality parameters are influenced by the high natural variability of water level, exceeding anthropogenic variability, and causing large uncertainty to the assessment of ecological status. Correction of metric values used for the assessment of ecological status for the effect of natural water level fluctuation reduces the signal-to-noise ratio in data and decreases the uncertainty of the status estimate. Here we have explored the potential to create synergy between optical and altimetry data for more accurate estimation of ecological status class of lakes. We have combined data from Sentinel-3 Synthetic Aperture Radar Altimeter and Cryosat-2 SAR Interferometric Radar Altimeter to derive water level estimations in order to apply corrections for chlorophyll a, phytoplankton biomass, and Secchi disc depth estimations from Sentinel-3 Ocean and Land Color Instrument data. Long-term in situ data was used to develop the methodology for the correction of water quality data for the effects of water level applicable on the satellite data. The study shows suitability and potential to combine optical and altimetry data to support in situ measurements and thereby support lake monitoring and management. Combination of two different types of satellite data from the continuous Copernicus program will advance the monitoring of lakes and improves the estimation of ecological status under European Union Water Framework Directive.

Phytoplankton primary production (PP) in lakes play an important role in the global carbon cycle. However, monitoring the PP in lakes with traditional complicated and costly in situ sampling methods are impossible due to the large number of lakes worldwide (estimated to be 117 million lakes). In this study, bio-optical modelling and remote sensing data (Sentinel-3 Ocean and Land Colour Instrument) was combined to investigate the spatial and temporal variation of PP in four Baltic lakes during 2018. The model used has three input parameters: concentration of chlorophyll-a, the diffuse attenuation coefficient, and incident downwelling irradiance. The largest of our studied lakes, Võrtsjärv (270 km2), had the highest total yearly estimated production (61 Gg C y−1) compared to the smaller lakes Lubans (18 Gg C y−1) and Razna (7 Gg C y−1). However, the most productive was the smallest studied, Lake Burtnieks (40.2 km2); although the total yearly production was 13 Gg C y−1, the daily average areal production was 910 mg C m−2 d−1 in 2018. Even if lake size plays a significant role in the total PP of the lake, the abundance of small and medium-sized lakes would sum up to a significant contribution of carbon fixation. Our method is applicable to larger regions to monitor the spatial and temporal variability of lake PP.

Currently, water monitoring programs are mainly based on in situ measurements; however, this approach is time-consuming, expensive, and may not reflect the status of the whole water body. The availability of Multispectral Imager (MSI) and Ocean and Land Colour Instrument (OLCI) free data with high spectral, spatial, and temporal resolution has increased the potential of adding remote sensing techniques into monitoring programs, leading to improvement of the quality of monitoring water. This study introduced an optical water type guided approach for boreal regions inland and coastal waters to estimate optical water quality parameters, such as the concentration of chlorophyll-a (Chl-a) and total suspended matter (TSM), the absorption coefficient of coloured dissolved organic matter at a wavelength of 442 nm (aCDOM(442)), and the Secchi disk depth, from hyperspectral, OLCI, and MSI reflectance data. This study was based on data from 51 Estonian and Finnish lakes and from the Baltic Sea coastal area, which altogether were used in 415 in situ measurement stations and covered a wide range of optical water quality parameters (Chl-a: 0.5−215.2 mg·m−3; TSM: 0.6−46.0 mg·L−1; aCDOM(442): 0.4−43.7 m−1; and Secchi disk depth: 0.2−12.2 m). For retrieving optical water quality parameters from reflectance spectra, we tested 132 empirical algorithms. The study results describe the best algorithm for each optical water type for each spectral range and for each optical water quality parameter. The correlation was high, from 0.87 up to 0.93, between the in situ measured optical water quality parameters and the parameters predicted by the optical water type guided approach.

The Sentinel-3 mission launched its first satellite Sentinel-3A in 2016 to be followed by Sentinel-3B and Sentinel-3C to provide long-term operational measurements over Earth. Sentinel-3A and 3B are in full operational status, allowing global coverage in less than two days, usable to monitor optical water quality and provide data for environmental studies. However, due to limited ground truth data, the product quality has not yet been analyzed in detail with the fiducial reference measurement (FRM) dataset. Here, we use the fully characterized ground truth FRM dataset for validating Sentinel-3A Ocean and Land Colour Instrument (OLCI) radiometric products over optically complex Estonian inland waters and Baltic Sea coastal areas. As consistency between satellite and local data depends on uncertainty in field measurements, filtering of the in situ data has been made based on the uncertainty for the final comparison. We have compared various atmospheric correction methods and found POLYMER (POLYnomial-based algorithm applied to MERIS) to be most suitable for optically complex waters under study in terms of product accuracy, amount of usable data and also being least influenced by the adjacency effect.

Total suspended solids (TSS) concentration is an important biogeochemical parameter for water quality management and sediment-transport studies. In this study, we propose a novel semi-analytical method for estimating TSS in clear to extremely turbid waters from remote-sensing reflectance (Rrs). The proposed method includes three sub-algorithms used sequentially. First, the remotely sensed waters are classified into clear (Type I), moderately turbid (Type II), highly turbid (Type III), and extremely turbid (Type IV) water types by comparing the values of Rrs at 490, 560, 620, and 754 nm. Second, semi-analytical models specific to each water type are used to determine the particulate backscattering coefficients (bbp) at a corresponding single wavelength (i.e., 560 nm for Type I, 665 nm for Type II, 754 nm for Type III, and 865 nm for Type IV). Third, a specific relationship between TSS and bbp at the corresponding wavelength is used in each water type. Unlike other existing approaches, this method is strictly semi-analytical and its sub-algorithms were developed using synthetic datasets only. The performance of the proposed method was compared to that of three other state-of-the-art methods using simulated (N = 1000, TSS ranging from 0.01 to 1100 g/m3) and in situ measured (N = 3421, TSS ranging from 0.09 to 2627 g/m3) pairs of Rrs and TSS. Results showed a significant improvement with a Median Absolute Percentage Error (MAPE) of 16.0% versus 30.2–90.3% for simulated data and 39.7% versus 45.9–58.1% for in situ data, respectively. The new method was subsequently applied to 175 MEdium Resolution Imaging Spectrometer (MERIS) and 498 Ocean and Land Colour Instrument (OLCI) images acquired in the 2003–2020 timeframe to produce long-term TSS time-series for Lake Suwa and Lake Kasumigaura, Japan. Performance assessments using MERIS and OLCI matchups showed good agreements with in situ TSS measurements.

[White paper] Water quality metrics derived from satellite observation can complement conventional water sampling, particularly to achieve much improved spatialand temporal coverage of medium (several square kilometres) and largerwaterbodies. Thus, it has the potential to enhance confidence in WFDecological status classification, firstly by quantifying elements of environmental status that are currently not or under-reported by Member States, such as the frequency, onset, duration and extent of phytoplankton blooms. Second,confidence in ecological status assessment would improve with increasedrepresentativeness of the natural diversity of waterbodies that aremonitored, their inter-annual variability and water quality trends within largerwaterbodies. Moreover, using standardised approaches, it would allow better comparison and standardization of water quality assessment across Member States, facilitating the management of transboundary waters in particular. Finally, by increasing spatial and temporal coverage, satellite observation is expected to enhance the effectiveness of the Programme of Measures (PoM) through early detection of deterioration, improving knowledge of the potentialextent of an impact, improving monitoring of the effectiveness of PoMs and providing information to support more strategic in situ sampling. The European Union and European Space Agency currently boast the mostadvanced suite of satellite-based instruments designed to observe optical water quality. The Copernicus framework of sensors and services has hadsignificant investment in recent years. Therefore, the vast majority of the costassociated with satellite-based monitoring of surface waters has already been invested. To promote and support the use of satellite-based water quality metrics in WFD statutory monitoring and reporting activities, we make the following recommendations, particularly in light of the ongoing revision of the WFD: Recognition of satellite observation as an assessment method in the context of the revision of the Water Framework Directive. Explicit encouragement to use satellite-based monitoring to complement national and statutory monitoring and reporting, such as already exercised by a limited number of countries (examplesin this paper) and available from existing academic, governmental and private sector capabilities, will provide a clear signal to Member States that its use is supported. In particular, satellite products that enhance confidence in the classification of phytoplankton biomass (typically measured by chlorophyll-a) by vastly improving spatial and temporal coverage should be considered, since these are already highly mature and can support quality elements that have thus far been considered too costly to include using conventional methods, such as assessing the frequency and intensity of algal blooms in lakes and coastal waters. Create a satellite observation expert group to harmonise metrics across countries and advise member states on best practises. The satellite observation expert group will: ensure harmonisation of the applicable satellite observation methods and their comparability with nationally-approved and intercalibrated methods; establish guidelines on how observation uncertainties should be reported; andensure close collaboration with the Water Framework Directive Common ImplementationStrategy working group on ecological status (WG ECOSTAT). An expert group advising on bestpractise is necessary because satellite-based observation capabilities continue to improve overtime whereas water quality management relies on stable and transparent methodologies. The expert group should work towards self-certification in the industry, including representationfrom the downstream Earth observation service sector, and be led by an independent researchand policy advisory body (such as the Joint Research Centre). Reference the use of satellite-based Earth observation metrics in the Reporting Guidance (Annex 5) of the revised Water Framework Directive. Particular reference to the use of satellite-derived water quality indicators in assessing phytoplankton biomass (by proxy of chlorophyll-a) and the frequency and intensity ofphytoplankton blooms in Annex 5 as well as national and international standards will ensurethe provision of monitoring data of equivalent scientific quality and comparability. Convene a conference for EC, Member States, WFD authorities to agree onrecommendations of common practices and reporting standards when using satellitebasedwater quality metrics to support the Water Framework Directive. Provide an opportunity for policy makers to recognise and proactively support the use of already available satellite-based Earth observation derived metrics and capitalise on alreadyestablished networks of national Earth observation scientists applying relevant derived metricsto the Water Framework Directive requirements.

An intercomparison of radiance and irradiance ocean color radiometers (The Second Laboratory Comparison Exercise—LCE-2) was organized within the frame of the European Space Agency funded project Fiducial Reference Measurements for Satellite Ocean Color (FRM4SOC) May 8−13, 2017 at Tartu Observatory, Estonia. LCE-2 consisted of three sub-tasks: 1) SI-traceable radiometric calibration of all the participating radiance and irradiance radiometers at the Tartu Observatory just before the comparisons; 2) Indoor intercomparison using stable radiance and irradiance sources in controlled environment; and 3) Outdoor intercomparison of natural radiation sources over terrestrial water surface. The aim of the experiment was to provide one link in the chain of traceability from field measurements of water reflectance to the uniform SI-traceable calibration, and after calibration to verify whether different instruments measuring the same object provide results consistent within the expected uncertainty limits. This paper describes the activities and results of the first two phases of LCE-2: the SI-traceable radiometric calibration and indoor intercomparison, the results of outdoor experiment are presented in a related paper of the same journal issue. The indoor experiment of the LCE-2 has proven that uniform calibration just before the use of radiometers is highly effective. Distinct radiometers from different manufacturers operated by different scientists can yield quite close radiance and irradiance results (standard deviation s < 1%) under defined conditions. This holds when measuring stable lamp-based targets under stationary laboratory conditions with all the radiometers uniformly calibrated against the same standards just prior to the experiment. In addition, some unification of measurement and data processing must be settled. Uncertainty of radiance and irradiance measurement under these conditions largely consists of the sensor’s calibration uncertainty and of the spread of results obtained by individual sensors measuring the same object.

An intercomparison of radiance and irradiance ocean color radiometers (the second laboratory comparison exercise—LCE-2) was organized within the frame of the European Space Agency funded project Fiducial Reference Measurements for Satellite Ocean Color (FRM4SOC) May 8–13, 2017 at Tartu Observatory, Estonia. LCE-2 consisted of three sub-tasks: (1) SI-traceable radiometric calibration of all the participating radiance and irradiance radiometers at the Tartu Observatory just before the comparisons; (2) indoor, laboratory intercomparison using stable radiance and irradiance sources in a controlled environment; (3) outdoor, field intercomparison of natural radiation sources over a natural water surface. The aim of the experiment was to provide a link in the chain of traceability from field measurements of water reflectance to the uniform SI-traceable calibration, and after calibration to verify whether different instruments measuring the same object provide results consistent within the expected uncertainty limits. This paper describes the third phase of LCE-2: The results of the field experiment. The calibration of radiometers and laboratory comparison experiment are presented in a related paper of the same journal issue. Compared to the laboratory comparison, the field intercomparison has demonstrated substantially larger variability between freshly calibrated sensors, because the targets and environmental conditions during radiometric calibration were different, both spectrally and spatially. Major differences were found for radiance sensors measuring a sunlit water target at viewing zenith angle of 139° because of the different fields of view. Major differences were found for irradiance sensors because of imperfect cosine response of diffusers. Variability between individual radiometers did depend significantly also on the type of the sensor and on the specific measurement target. Uniform SI traceable radiometric calibration ensuring fairly good consistency for indoor, laboratory measurements is insufficient for outdoor, field measurements, mainly due to the different angular variability of illumination. More stringent specifications and individual testing of radiometers for all relevant systematic effects (temperature, nonlinearity, spectral stray light, etc.) are needed to reduce biases between instruments and better quantify measurement uncertainties.

An intercomparison of radiance and irradiance ocean color radiometers (the second laboratory comparison exercise--LCE-2) was organized within the frame of the European Space Agency funded project Fiducial Reference Measurements for Satellite Ocean Color (FRM4SOC) May 8-13, 2017 at Tartu Observatory, Estonia. LCE-2 consisted of three sub-tasks: (1) SI-traceable radiometric calibration of all the participating radiance and irradiance radiometers at the Tartu Observatory just before the comparisons; (2) indoor, laboratory intercomparison using stable radiance and irradiance sources in a controlled environment; (3) outdoor, field intercomparison of natural radiation sources over a natural water surface. The aim of the experiment was to provide a link in the chain of traceability from field measurements of water reflectance to the uniform SI-traceable calibration, and after calibration to verify whether different instruments measuring the same object provide results consistent within the expected uncertainty limits. This paper describes the third phase of LCE-2: The results of the field experiment. The calibration of radiometers and laboratory comparison experiment are presented in a related paper of the same journal issue [1]. Compared to the laboratory comparison, the field intercomparison has demonstrated substantially larger variability between freshly calibrated sensors, because the targets and environmental conditions during radiometric calibration were different, both spectrally and spatially. Major differences were found for radiance sensors measuring a sunlit water target at viewing zenith angle of 139° because of the different fields of view. Major differences were found for irradiance sensors because of imperfect cosine response of diffusers. Variability between individual radiometers did depend significantly also on the type of the sensor and on the specific measurement target. Uniform SI traceable radiometric calibration ensuring fairly good consistency for indoor, laboratory measurements is insufficient for outdoor, field measurements, mainly due to the different angular variability of illumination. More stringent specifications and individual testing of radiometers for all relevant systematic effects (temperature, nonlinearity, spectral stray light, etc.) are needed to reduce biases between instruments and better quantify measurement uncertainties.

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.

Consistent, cross-mission retrievals of near-surface concentration of chlorophyll-a (Chla) in various aquatic ecosystems with broad ranges of trophic levels have long been a complex undertaking. Here, we introduce a machine-learning model, the Mixture Density Network (MDN), that largely outperforms existing algorithms when applied across different bio-optical regimes in inland and coastal waters. The model is trained and validated using a sizeable database of co-located Chla measurements (n = 2943) and in situ hyperspectral radiometric data resampled to simulate the Multispectral Instrument (MSI) and the Ocean and Land Color Imager (OLCI) onboard Sentinel-2A/B and Sentinel-3A/B, respectively. Our performance evaluations of the model, via two-thirds of the in situ dataset with Chla ranging from 0.2 to 1209 mg/m3 and a mean Chla of 21.7 mg/m3, suggest significant improvements in Chla retrievals. For both MSI and OLCI, the mean absolute logarithmic error (MAE) and logarithmic bias (Bias) across the entire range reduced by 40–60%, whereas the root mean squared logarithmic error (RMSLE) and the median absolute percentage error (MAPE) improved two-to-three times over those from the state-of-the-art algorithms. Using independent Chla matchups (n

Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains. © 2018 by the authors. Licensee MDPI, Basel, Switzerland., The authors acknowledge COST Action ES 1105 “CYANOCOST—Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management” and COST Action ES 1201 “NETLAKE—Networking Lake Observatories in Europe” for contributing to this study through networking and knowledge sharing with European experts in the field. Evanthia Mantzouki was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation (SERI) to Bas Ibelings and by supplementary funding from the University of Geneva. We thank Clare Ahnlund, Ena Suarez and Irene Gallego for helping out with the Swiss survey. We thank Wendy Beekman and Els J. Faassen for the nutrient and toxin analysis.

Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment., The authors acknowledge COST Action ES 1105 “CYANOCOST – Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management” and COST Action ES 1201 “NETLAKE – Networking Lake Observatories in Europe” for contributing to this study through networking and knowledge sharing with European experts in the field. Evanthia Mantzouki was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation (SERI) to Bas Ibelings and by supplementary funding from University of Geneva. We thank Wendy Beekman for the nutrient analysis and the University of Wageningen for covering the costs of this analysis from the personal funding of dr. Miquel Lürling. We thank Pieter Slot for assisting with the pigment analysis and the University of Amsterdam for covering the costs of the analysis through funding from the group of Prof. Jef Huisman and dr. Petra Visser (IBED). We would like to thank the Environmental Data Initiative for covering the cost of archiving the EMLS dataset. We would like to thank the Leibniz Institute of Freshwater Ecology and Inland Fisheries, Dept. of Experimental Limnology and the Aquatic Microbial Ecology Group for logistic and technical support of J. Fonvielle and H.-P. Grossart; and the Leibniz Association for financial support. The collection of data for Lough Erne and Lough Neagh were funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland.

The need to restore and protect waterbodies from further degradation has resulted in formulation of the European Union Water Framework Directive 2000/60/EC WFD. The directive aims to harmonize European legislation on water; and member states shall establish a programme for monitoring the status of all waterbodies larger than 0.5 km2, in order to ensure future quality and quantity of inland waters. The biological and physical–chemical status and ecological potential should be assessed and action plans for a sustainable management and protection of freshwater resources should be established. In practice, this means that extensive and expensive sampling programmes are needed. The ecological status of a waterbody can be described by various biological and physical–chemical quality elements, and several of these important ecological parameters can be monitored by space-based instruments: 1 phytoplankton biomass; 2 chlorophyll-a concentration; 3 water transparency; and 4 frequency and intensity of blooms. The objective of this article is to demonstrate how Environmental Satellite/Medium Resolution Imaging Spectrometer and future Sentinel-3/Ocean Land Colour Instrument data can be effectively used to complement traditional water monitoring programmes by adding information with significantly improved spatial coverage and temporal detail to support the WFD status assessment process. Examples are provided for five large European lakes Peipsi, Vortsjarv, Vanern, Vattern, Malaren. Time series based on satellite data and data collected within national and regional monitoring programmes were compiled and compared, to demonstrate good agreement between the two techniques, but also to discuss natural differences and limitations. Furthermore, the ecological status class based on satellite and in situ data for each waterbody was calculated and analysed.

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 (

In a 3 wk Baltic Sea coastal experiment artificial N and P limitation were studied in 9 mesocosms, 51 m 3 each, filled with a natural summer plankton community. The initial situation (molar dissolved N:P ratio of 0.9; zooplankton to phytoplankton biomass ratio of 2.8) was boosted with 5 daily N and P additions in Redfield ratio, to increase algal biomass and demand for nutrients. Thereafter, either N or P limitation was induced by cutting one element, while supplying the other. Discontinu- ing N supply resulted in lower phytoplankton biomass (as chlorophyll a and wet weight), but more bloom-forming, N2-fixing filamentous cyanobacteria. Stable C:N and N:P ratios of organic particles and the increase of total nitrogen indicated an average N2-fixation rate of 3.3 to 7.4 mmol N m -2 d -1 , which by the end of the experiment equalised the total N in the mesocosms with and without N addi- tion. Discontinuing P supply resulted in higher algal biomass, and the particulate organic matter with increasing molar C:P (from 90 to 300) and N:P ratios (from 16 to 50) suggested bulk level P shortage. The biomass response distinguished 3 groups of phytoplankton, each containing filamentous cyanobacterial species that are considered: (1) nitrogen limited, e.g. chlorophytes, non-heterocystous filamentous cyanobacteria Pseudanabaena spp. and colonial cyanobacteria (e.g. Snowella sp., Cyanodictyon sp.); (2) phosphorus limited, e.g. the N2-fixers Anabaena spp. and Nodularia spumi- gena; and (3) indifferent species, e.g. the N2-fixer Aphanizomenon sp. and heterotrophic and oppor- tunistic flagellates. Aphanizomenon sp. — the dominant species in the experiment — increased equally in all mesocosms at the expense of fixed N and internal P reserves. Our results highlight the diverse nutritional and growth strategies of the bloom-forming cyanobacteria and suggest that eutrophication management decisions in the Baltic Sea should inevitably consider simultaneous reduction of both N and P.

A strong biomass increase of two Anabaena species was observed in natural plankton community enclosed into nine large mesocosms (51 m 3 ) and manipulated with mineral nutrients and an organic carbon source during a 3-week period in the coastal Baltic Sea. The water column and settled material from the bottom of the mesocosms were sampled at 2-day intervals. Planktonic populations of Anabaena lemmermannii Richter and A. cylindrica Lemmermann and sedimentation rates of akinetes to the bottom were quantified. Comparing mesocosms with artificially induced nitrogen and phosphorus limitation, we found that during the third week of the experiment, the population size of A. lemmermannii was clearly higher in nitrogen-limited units (by a factor of 2.4), whereas the production rate of akinetes was higher in the phosphorus-limited units (by a factor of 2.5). Input of freshly produced A. lemmermannii akinetes to the benthos was on average 15 x 10 6 and 6 × 10 6 cells · m -2 · d -1 in the P - and N - limited mesocosms, respectively. Our estimates of specific akinete production rate of A. lemmermannii in P - and N - limited mesocosms revealed an even larger divergence (a factor of 5.5), being on average 2.4 and 0.4 akinetes ·10 -3 vegetative cells -1 · d -1 , respectively. The phosphorus addition effectively reduced akinete production of A. lemmermannii. Differences in the nutrient manipulation had no apparent effect on the biomass and akinete production of A. cylindrica. The akinete production pattern of A. cylindrica revealed a 1-week delay compared with the vegetative population peak, whereas such a delay was not obvious in A. lemmermannii.

Thermal and chemical regime and phytoplankton development in hypertrophic sharply stratified L. Verevi (S-E Estonia) were studied from April to October 2000. The lake stratified shortly after the ice break-up in April. Even in the homothermal conditions in October the lake remained chemically and biologically stratified. Limnothrix redekei being a minor component of the cyanobacterial community, reached its maximum (1.4 g.m -3 ) in the metalimnion in May. The biomass peak of the dominating Plankothrix agardhii followed in July (37.6 g.m -3 ). The biomass maximum of L. redekei was reached in cooler water at lower nitrogen and phosphorus concentrations compared with P agardhii. Light conditions and the total N: total P ratio in the layer of the biomass peaks were similar. Nitrogen limitation was suggested as the main reason for the observed seasonal succession of the two cyanobacterial species.

Changes in the phytoplankton community of the hypertrophic, sharply stratified Lake Verevi have been studied over eight decades. Due to irregular discharge of urban wastewater, the trophic state of the lake has changed from moderately eutrophic to hypertrophic. We found that the trophic state in summer increased in the 1980s and remained at a hypertrophic level since then. Planktothrix agardhii was recorded first in the 1950s and became the dominant species in the 1980s, forming biomass maxima under the ice and in the metalimnion during the vegetation period. In summer 1989, P. agardhii contributed almost 100% of the phytoplankton biomass. Generally, the highest biomass values occurred in the metalimnion. In spring, when P. agardhii was less numerous, diatoms and cryptophytes prevailed. In springs 2000 and 2001 different diatoms dominated – Synedra acus var. angustissima (18.6 g m−3) and Cyclostephanos dubius (9.2 g m−3), respectively. In recent years, the spring overturn has been absent. In the conditions of strong thermal stratification sharp vertical gradients of light and nutrients caused a large number of vertically narrow niches in the water column. During a typical summer stage, the epilimnion, dominated by small flagellated chrysophytes, is nearly mesotrophic, and water transparency may reach 4 m. The lower part of the water column is hypertrophic with different species of cryptophytes and euglenophytes. A characteristic feature is the higher diversity of Chlorococcales. Often, species could form their peaks of biomass in very narrow layers, e.g. in August 2001 Ceratium hirundinella (18.6 g m−3) was found at a depth of 5 m (the lower part of the metalimnion with hypoxic conditions), Cryptomonas spp. (56 g m−3) at 6 m (with traces of oxygen and a relatively high content of dissolved organic matter) and euglenophytes (0.6 g m−3) at 7 m and deeper (without oxygen and a high content of dissolved organic matter).

Lake Verevi (12.6 ha, maximum depth 11.0 m, mean depth 3.6 m) is a strongly eutrophic and stratified lake. Planktothrix agardhii is the most characteristic phytoplankton species in summer and autumn, while photosynthesizing sulphur bacteria can occur massively in the metalimnion. Primary production (PP) and chlorophyll a concentration (Chl a) were seasonally studied in 1991, 1993, 2000, and 2001. Vertical distribution of PP was rather complex, having usually two peaks, one at or near the surface (0–1 m), and another deeper (at 3–7 m) in the metalimnion. The values of dark fixation of CO2 in the metalimnion were in most cases higher than those in the upper water layer. Considering the average daily PP 896 mg C m−2 and yearly PP 162 mg C m−2, Secchi depth 2.34 m, and epilimnetic concentrations of chlorophyll a (19.6 mg m−3), total nitrogen and total phosphorus (TP, 52 mg m−3) in 2000, L. Verevi is a eutrophic lake of a ‘good’ status. Considering the total amounts of nutrients stored in the hypolimnion, the average potential concentrations in the whole water column could achieve 1885 mg m−3 of TN and 170 mg m−3 of TP reflecting hypertrophic conditions and a ‘bad’ status. Improvement of the epilimnetic water quality from the 1990s to the 2000s may have resulted from incomplete spring mixing and might not reflect the real improvement. A decreased nutrient concentration in the epilimnion has supported the establishment of a ‘clear epilimnion state’ allowing light to penetrate into the nutrient-rich metalimnion and sustaining a high production of cyanobacteria and phototrophic sulphur bacteria.

The epilimnetic phytoplankton and its relations to nutrient content in Lake Verevi through the whole vegetation period in 2000 were studied. Lake Verevi (surface 12.6 ha, mean depth 3.6 m, maximum depth 11 m) is a hypertrophic hard-water lake, where the so-called spring meromixis occurs due to an extremely warm spring. Most dissolved nutrients in the epilimnion were low already in spring, and their concentrations were quite stable during the study period. The concentration of total silicon was very low in spring but increased rapidly in summer. Total phosphorus followed the pattern for stratified eutrophic lakes, and total nitrogen was quite high. The stoichiometric N:P ratio fluctuated between 25 and 81. The dynamics of phytoplankton biomass with a spring peak from April to May and a late summer peak from July to August is typical of Estonian eutrophic lakes. Green algae and chrysophytes occurred in the phytoplankton throughout the vegetation period. The spring peak was dominated by diatoms (Synedra ulna and Synedra acus var. angustissima) and the summer peak was caused by Aphanizomenon klebahnii and Ceratium hirundinella. The study showed that in physically stratified systems, the total concentration of limiting resources and plain physical factors (light and temperature) may be more important in the determination of phytoplankton dominants than different resource ratios. A combination of light and temperature optimum, along with nutrient utilization and transport capacity, effectively segregates phytoplankton species and can be used for the explanation of seasonal succession pattern.

The Maximum Chlorophyll Index (MCI), developed for the MERIS sensor processing scheme, is used to investigate the seasonaldynamics, spatial distribution, and coverage of cyanobacterial blooms over Lake Peipsi (Estonia/Russia) and Lake Võrtsjärv(Estonia). In these optically complex waters, the amounts of suspended matter and dissolved organic matter vary greatly andindependently of the phytoplankton biomass. We demonstrate that MCI is a useful, new tool for detecting and estimating cyanobacterialbiomass (R2 = 0.73), phytoplankton biomass (R2 = 0.70) and chlorophyll a concentration (R2 = 0.64). The MCI-derivedresults are consistent with known patterns of phytoplankton dynamics in these lakes, whose optical properties are in the same range as in many coastalregions of the Baltic Sea.

[White paper] Water quality metrics derived from satellite observation can complement conventional water sampling, particularly to achieve much improved spatialand temporal coverage of medium (several square kilometres) and largerwaterbodies. Thus, it has the potential to enhance confidence in WFDecological status classification, firstly by quantifying elements of environmental status that are currently not or under-reported by Member States, such as the frequency, onset, duration and extent of phytoplankton blooms. Second,confidence in ecological status assessment would improve with increasedrepresentativeness of the natural diversity of waterbodies that aremonitored, their inter-annual variability and water quality trends within largerwaterbodies. Moreover, using standardised approaches, it would allow better comparison and standardization of water quality assessment across Member States, facilitating the management of transboundary waters in particular. Finally, by increasing spatial and temporal coverage, satellite observation is expected to enhance the effectiveness of the Programme of Measures (PoM) through early detection of deterioration, improving knowledge of the potentialextent of an impact, improving monitoring of the effectiveness of PoMs and providing information to support more strategic in situ sampling. The European Union and European Space Agency currently boast the mostadvanced suite of satellite-based instruments designed to observe optical water quality. The Copernicus framework of sensors and services has hadsignificant investment in recent years. Therefore, the vast majority of the costassociated with satellite-based monitoring of surface waters has already been invested. To promote and support the use of satellite-based water quality metrics in WFD statutory monitoring and reporting activities, we make the following recommendations, particularly in light of the ongoing revision of the WFD: Recognition of satellite observation as an assessment method in the context of the revision of the Water Framework Directive. Explicit encouragement to use satellite-based monitoring to complement national and statutory monitoring and reporting, such as already exercised by a limited number of countries (examplesin this paper) and available from existing academic, governmental and private sector capabilities, will provide a clear signal to Member States that its use is supported. In particular, satellite products that enhance confidence in the classification of phytoplankton biomass (typically measured by chlorophyll-a) by vastly improving spatial and temporal coverage should be considered, since these are already highly mature and can support quality elements that have thus far been considered too costly to include using conventional methods, such as assessing the frequency and intensity of algal blooms in lakes and coastal waters. Create a satellite observation expert group to harmonise metrics across countries and advise member states on best practises. The satellite observation expert group will: ensure harmonisation of the applicable satellite observation methods and their comparability with nationally-approved and intercalibrated methods; establish guidelines on how observation uncertainties should be reported; andensure close collaboration with the Water Framework Directive Common ImplementationStrategy working group on ecological status (WG ECOSTAT). An expert group advising on bestpractise is necessary because satellite-based observation capabilities continue to improve overtime whereas water quality management relies on stable and transparent methodologies. The expert group should work towards self-certification in the industry, including representationfrom the downstream Earth observation service sector, and be led by an independent researchand policy advisory body (such as the Joint Research Centre). Reference the use of satellite-based Earth observation metrics in the Reporting Guidance (Annex 5) of the revised Water Framework Directive. Particular reference to the use of satellite-derived water quality indicators in assessing phytoplankton biomass (by proxy of chlorophyll-a) and the frequency and intensity ofphytoplankton blooms in Annex 5 as well as national and international standards will ensurethe provision of monitoring data of equivalent scientific quality and comparability. Convene a conference for EC, Member States, WFD authorities to agree onrecommendations of common practices and reporting standards when using satellitebasedwater quality metrics to support the Water Framework Directive. Provide an opportunity for policy makers to recognise and proactively support the use of already available satellite-based Earth observation derived metrics and capitalise on alreadyestablished networks of national Earth observation scientists applying relevant derived metricsto the Water Framework Directive requirements.