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Multiple stressors, such as overfishing, pollution, climate change, biological invasions etc., are affecting fish communities, and thus can have versatile effects on marine ecosystems and socio-economic activities as well. Understanding the changes in the fish community structure is ecologically and economically important, yet a very complex issue, requiring comprehensive analysis of multiple factors. The role of regional oceanographic variability, namely, coastal upwelling, is often neglected when it comes to the analysis of fish assemblages. In this perspective, we were aiming, for the first time in the Baltic Sea, to assess the upwelling influence on fish communities and fish community-based ecological indices used under Marine Strategy Framework Directive. The study covered a long-term period (2000–2019) for upwelling identified by satellite data analysis and fish gillnet surveys, performed in three distinct locations in the coastal waters of the SE Baltic Sea. Overall, our study revealed that temporal dynamics of fish abundance and community composition were associated with the presence of coastal upwelling. The study outcomes suggest that the fish community was more diverse and a higher number of some fish species was observed before upwelling. During upwelling, there was more evident dominance of 1–2 main marine fish species. Through the changes in fish abundance and species composition upwelling was also responsible for the changes in fish community structure-based indices for marine environment status, i.e., in the majority of the cases a decrease in Trophic, Piscivorous Fish, and Diversity indices were observed. Our study demonstrates that upwelling can affect both, the quantitative and qualitative characteristics of coastal fish communities, therefore, it is important to consider this when predicting shifts in the distribution of fish stocks or assessing environmental status indicators, especially under changing climate. We believe that our approach adds novel information to the study of coastal ecosystems of the Baltic Sea and is important for better management of socio-economic activities in the coastal zone. Keywords: upwelling; SST; fish community; ecological indices; good environmental status (GES); marine ecosystems.

Coastal lagoons are important sites for nitrogen (N) removal via sediment burial and denitrification. Blooms of heterocystous cyanobacteria may diminish N retention as dinitrogen (N2) fixation offsets atmospheric losses via denitrification. We measured N2 fixation in the Curonian Lagoon, Europe's largest coastal lagoon, to better understand the factors controlling N2 fixation in the context of seasonal changes in phytoplankton community composition and external N inputs. Temporal patterns in N2 fixation were primarily determined by the abundance of heterocystous cyanobacteria, mainly Aphanizomenon flos-aquae, which became abundant after the decline in riverine nitrate inputs associated with snowmelt. Heterocystous cyanobacteria dominated the summer phytoplankton community resulting in strong correlations between chlorophyll a (Chl a) and N2 fixation. We used regression models relating N2 fixation to Chl a, along with remote-sensing-based estimates of Chl a to derive lagoon-scale estimates of N2 fixation. N2 fixation by pelagic cyanobacteria was found to be a significant component of the lagoon's N budget based on comparisons to previously derived fluxes associated with riverine inputs, sediment–water exchange, and losses via denitrification. To our knowledge, this is the first study to derive ecosystem-scale estimates of N2 fixation by combining remote sensing of Chl a with empirical models relating N2 fixation rates to Chl a.

This study presents an assessment of PRISMA (PRecursore IperSpettrale della Missione Applicativa) for water applications, by including a general description of the mission and by focusing on the standard Level 1 (L1) and Level 2 (L2) products acquired on different aquatic systems. A preliminary analysis on the estimation of signal-to-noise ratio (SNR) from L1 PRISMA products in the visible near infrared spectra (VISNIR) is indicating values comparable to Sentinel-2 MSI from literature, apart at short wavelengths where PRISMA SNR is lower. Few examples of L2 products in terms of water reflectance are also presented to encourage the exploitation of PRISMA for aquatic ecosystem mapping. The results of this study are indicating that even if some applications might be developed with the standard L2 products, an ad-hoc processing might be necessary to include the specific requirements of atmospheric correction of water targets. Further analyses with a higher number of imagery data are however recommended to fully characterize the PRISMA products.

Coastal lagoons are important sites for nitrogen (N) removal via sediment burial and denitrification. Blooms of heterocystous cyanobacteria may diminish N retention as dinitrogen (N2) fixation offsets atmospheric losses via denitrification. We measured N2 fixation in the Curonian Lagoon, Europe's largest coastal lagoon, to better understand the factors controlling N2 fixation in the context of seasonal changes in phytoplankton community composition and external N inputs. Temporal patterns in N2 fixation were primarily determined by the abundance of heterocystous cyanobacteria, mainly Aphanizomenon flosaquae, which became abundant after the decline in riverine nitrate inputs associated with snowmelt. Heterocystous cyanobacteria dominated the summer phytoplankton community resulting in strong correlations between chlorophyll-a (Chl-a) and N2 fixation. We used regression models relating N2 fixation to Chl-a, along with remote sensing-based estimates of Chl-a to derive lagoon-scale estimates of N2 fixation. N2 fixation by pelagic cyanobacteria was found to be a significant component of the lagoon's N budget based on comparisons to previously derived fluxes associated with riverine inputs, sediment-water exchange and losses via denitrification. To our knowledge, this is the first study to derive ecosystem-scale estimates of N2 fixation by combining remote sensing of Chl-a with empirical models relating N2 fixation rates to Chl-a.

Our goal was to understand how differences in source material (allochthonous vs. autochthonous) and phytoplankton communities (diatoms vs. cyanobacteria) influence composition and settling properties of suspended particulate matter. We characterized the composition and settling properties of suspended particulate matter in two systems—one which has a high hydrologic loading factor (watershed to surface area ratio), and a diatom-dominated phytoplankton community (James River Estuary, USA), and a second, where hydrologic inputs are proportionally smaller, and the summer phytoplankton community is dominated by cyanobacteria (Curonian Lagoon, Lithuania). In the James, we found that TSS concentrations were positively related to discharge, whereas POC concentrations were negatively correlated with discharge and positively correlated with Chl-a. We infer that suspended particulate matter in this system was largely derived from allochthonous inputs, but that the organic matter fraction was derived from autochthonous production. In the Curonian Lagoon, TSS concentrations were correlated with Chl-a, but not discharge, indicating that suspended particulate matter was largely of autochthonous origin. In the James, the proportion of settleable materials was greater during high TSS concentrations, indicating that high discharge events delivered heavier particulates. In the Curonian Lagoon, we observed a seasonal decline in settling rates associated with the shift from mixed (diatoms and chlorophytes) to cyanobacteria-dominated phytoplankton, which we attribute to the presence of positively buoyant cyanobacteria. We found that a comparative approach yielded useful insights regarding sources, composition, and settling properties of suspended particulate matter in two estuaries that differ in hydrologic loading and phytoplankton community composition. Our findings suggest that the presence of positively buoyant cyanobacteria favors export losses of particulate C, N, and P to marine waters over retention through sedimentation in transitional zones.

We combined a mass balance approach with measurements of air–water and sediment–water nitrogen (N) exchange to better understand the mechanisms attenuating N throughputs in a eutrophic coastal lagoon. We were particularly interested in how seasonal shifts in external versus internal N fluxes and the transition from diatom- to cyanobacteria- dominated phytoplankton communities influence N storage and loss to the atmosphere. We found that on an annual basis almost all of the N removed by the lagoon was due to sediment storage following the spring diatom bloom. This period was characterized by high riverine inputs of dissolved inorganic nitrogen, high rates of assimilatory conversion to particulate nitrogen (PN), and net accrual of N in sediments. By contrast, the larger summer bloom was associated with low sediment N storage, which we attribute in part to the presence of positively-buoyant cyanobacteria. Low settling rates during cyanobacteria blooms favored export of PN to the Baltic Sea over sediment accrual in the lagoon. In addition, summer dinitrogen (N2) fixation by cyanobacteria largely offset annual N2 losses via denitrification. These findings show that cyanobacteria blooms diminish N attenuation within the lagoon by altering the balance of N exchange with the atmosphere and by promoting export of particulate N over sediment burial.

Nutrient fluxes from land to sea are regulated by climatic factors governing hydrologic loading rates (e.g., storm events, snowmelt) and by internal processes within estuaries that affect nutrient transformation and retention. We compared monthly input and output fluxes of N, Si, and P at the entrance and exit of the hypereutrophic Curonian Lagoon to better understand how seasonal changes in the stoichiometry of nutrient inputs and the occurrence of algal blooms affected nutrient retention within the lagoon. Nutrient ratios were indicative of increasing Si and N limitation during the growing season, and these were associated with a shift from a diatom-based to a cyanobacteria dominated phytoplankton community. The estuary was a net sink for dissolved nutrients, but we observed large interannual difference in the overall retention of N and P. The occurrence of a large cyanobacteria bloom in 2012 was associated with increased export of particulate matter to the Baltic Sea resulting in a net surplus of P export. Bloom conditions mobilized P from sediments and resulted in a shift from net retention to net export for the lagoon. The findings of our study illustrate how changes in nutrient loading ratios influence phytoplankton community composition, which in turn alters the source-sink status of the estuary.

Aquatic birds may impact shallow ecosystems via organic and nutrient enrichment with feces. Such input may alleviate nutrient limitation, unbalance their ecological stoichiometry, and stimulate primary production. Herbivorous and piscivorous birds may produce different effects on aquatic ecosystems due to different physiology, diet and feces elemental composition. We analyze the effects of droppings from swans (herbivorous) and cormorants (piscivorous) on phytoplankton growth via a laboratory experiment. These birds are well represented in the Curonian Lagoon, where they form large colonies. As this lagoon displays summer algal hyper-blooms, we hypothesize an active, direct role of birds via defecation on algal growth. Short-term incubations of phytoplankton under low and high feces addition produces different stimulation of algal growth, significantly higher with high inputs of cormorant feces. The latter produces a major effect on reactive phosphorus concentration that augments significantly, as compared to treatments with swan feces, and determines an unbalanced, N-limited stoichiometry along with the duration of the experiment. During the incubation period, the dominant algal groups switch from blue-green to green algae, but such switch is independent of the level of feces input and from their origin. Heterotrophic bacteria also are stimulated by feces addition, but their increase is transient.

During the last eight years, airborne hyperspectral data were acquired over aquatic ecosystems with APEX, under the umbrella of EU FP7 funding (EUFAR and INFORM projects). APEX images were collected over shallow freshwater and coastal ecosystems, characterized by joint presence of phytoplankton in high concentrations and macrophytes, namely: Mantua lakes system (Italy), on 21 September 2011 and on 27 September 2014 (5 flight lines, 5 m resolution); Lake Hídvégi (Hungary), on 19 July 2014 (3 flight lines, 5 m resolution); and Curonian Lagoon (Lithuania), on 1 and 2 September 2016 (24 flight lines, 3 m resolution). Synchronous to airborne acquisitions, radiometric and eco-limnological parameters characterizing the three study sites were collected in situ in order to validate the APEX data and to calibrate reflectance-based models for mapping the biodiversity and abundance of primary producers. Semi-empirical and bio-optical models were applied to APEX derived surface reflectance images for estimating phytoplankton pigments concentration, such as Chlorophyll-a (Chl-a) and Phycocyanin (PC), and macrophyte coverage and traits. We derived detailed maps of Chl-a concentration as proxy of phytoplankton abundance and dominant phytoplankton functional type, being Diatoms or Cryptophytes/Cyanobacteria (Giardino et al., 2018). In addition, phytoplankton spatial patchiness was assessed and related to hydrodynamic features of Mantua lakes system (Pinardi et al., 2015), and multi-temporal analysis revealed lake areas characterized by strong Chl-a variation dynamics (Bresciani et al., 2017). Ecosystem-scale maps of macrophyte morphological traits, in terms of biomass and density, were produced (Villa et al., 2017), and coexistence and interactions between phytoplankton and macrophytes were investigated (Bolpagni et al., 2014). Our main aim is to aggregate all these results for demonstrating the high potential of airborne hyperspectral imaging platforms in providing high resolution, detailed and reliable information on different primary producers in complex aquatic ecosystems.

In recent years satellite water quality information have been used for several purposes, such as: 1) regular and specific monitoring, 2) matters that require Near Real Time information (e.g. when cyanobacterial blooms are threatening the swimming water quality) and 3) for the spatial optimisation of monitoring networks. To the aim, image processing chains need to be set up to transform the radiance recorded by satellite sensors into information on water quality, such as the concentrations of water constituents, the physical values on water surface temperature or maps depicting e.g. the spatial extent of aquatic vegetation. Despite these techniques have been developed since about three decades, there are still ongoing developments to produce accurate and consistent products across all water bodies.This is particularly the case for EOMORES, whose target lakes include a wide range of water types. Moreover, as EOMORES makes use of the latest generation of satellite sensors, consolidated image processing techniques need to be adapted according to the resolutions and spectral bands of these newest sensors. This is especially relevant for Sentinel-2 MSI,since for Sentinel-3 OLCI most of the developments are based on its precursor MERIS on Envisat (2002-2012).This document hence illustrates the image processing chain that have been adapted to produce relevant water quality information for the EOMORES study sites. A first section is dedicated to the description of the methods while the last part describe show the processors have been applied to produce maps (both of the past and recent years, including 2018) of water quality. The selected processors are now being used to set up the operational EOMORES service according to WP6.

Image correction for atmospheric effects (iCOR) is an atmospheric correction tool that can process satellite data collected over coastal, inland or transitional waters and land. The tool is adaptable with minimal effort to hyper- or multi-spectral radiometric sensors. By using a single atmospheric correction implementation for land and water, discontinuities in reflectance within one scene are reduced. iCOR derives aerosol optical thickness from the image and allows for adjacency correction, which is SIMilarity Environmental Correction (SIMEC) over water. This paper illustrates the performance of iCOR for Landsat-8 OLI and Sentinel-2 MSI data acquired over water. An intercomparison of water leaving reflectance between iCOR and Aerosol Robotic Network – Ocean Color provided a quantitative assessment of performance and produced coefficient of determination (R2) higher than 0.88 in all wavebands except the 865 nm band. For inland waters, the SIMEC adjacency correction improved results in the red-edge and near-infrared region in relation to optical in situ measurements collected during field campaigns.

The scope of this document is to report about the use of additional data the EOMORES project received via the Data Ware House(DWH) in 2018.Four EOMORES partners presents the results on the use of VHR data for lagoon, lakes, reservoirs and channels -small water bodies that not always can be monitored by means of the freely available Sentinel satellites data.

Phytoplankton blooms in internal water bodies are an unpleasant sight that often emerges on top like a layer of foam containing high concentrations of toxins (scum event). Monitoring the concentration of algae and the occurrence of scum in lakes and lagoons has become a topic of interest for management and science. Optical remote sensing is a validated tool but unfortunately it is highly hindered by clouds. For regions with frequent cloud cover, such as the Baltic region, this means loss of data, which limits the purpose of sensing to spatially and temporally characterize any scum for a comprehensive ecological analysis. The aim of this paper is to investigate whether the use of synthetic aperture radar (SAR) images can compensate for the weaknesses of optical images for cyanobacteria bloom monitoring purposes in the event of cloudy skies. A &ldquo, ready to use&rdquo, approach to detect cyanobacteria bloom in the Curonian Lagoon based on the level 2 ocean product of Sentinel-1 images is proposed. This method is empirically validated for the images of summer/autumn 2018 of the Curonian Lagoon.

There is an increasing understanding and requirement to take into account the effects of invasive alien species (IAS) in environmental quality assessments. While IAS are listed amongst the most important factors threatening marine biodiversity, information on their impacts remains unquantified, especially for phytoplankton species. This study attempts to assess the impacts of invasive alien phytoplankton in the Baltic Sea during 1980-2008. A bioinvasion impact assessment method (BPL - biopollution level index) was applied to phytoplankton monitoring data collected from eleven sub-regions of the Baltic Sea. BPL takes into account abundance and distribution range of an alien species and the magnitude of the impact on native communities, habitats and ecosystem functioning. Of the 12 alien/cryptogenic phytoplankton species recorded in the Baltic Sea only one (the dinoflagellate Prorocentrum minimum) was categorized as an IAS, causing a recognizable environmental effect.

Multi-sensor satellite data are used to assess cyanobacteria blooms in the Curonian Lagoon. The exploitation of SAR, in combination with optical data, is investigated to take full advantage from the all-weather, night/day SAR imaging capability. A dataset of images has been analyzed to: 1) study the effect of cyanobacteria on microwave signals; 2) assess the daily evolution of cyanobacteria bloom from multi-sensors data; and 3) evaluate the dependence of dynamics of blooms on winds. The results show a significant correlation (R 2 > 0.8, p

Marine chemical ecology comprises the study of the production and interaction of bioactive molecules affecting organism behavior and function. Here we focus on bioactive compounds and interactions associated with phytoplankton, particularly bloom-forming diatoms, prymnesiophytes and dinoflagellates. Planktonic bioactive metabolites are structurally and functionally diverse and some may have multiple simultaneous functions including roles in chemical defense (antipredator, allelopathic and antibacterial compounds), and/or cell-to-cell signaling (e. g., polyunsaturated aldehydes (PUAs) of diatoms). Among inducible chemical defenses in response to grazing, there is high species-specific variability in the effects on grazers, ranging from severe physical incapacitation and/or death to no apparent physiological response, depending on predator susceptibility and detoxification capability. Most bioactive compounds are present in very low concentrations, in both the producing organism and the surrounding aqueous medium. Furthermore, bioactivity may be subject to synergistic interactions with other natural and anthropogenic environmental toxicants. Most, if not all phycotoxins are classic secondary metabolites, but many other bioactive metabolites are simple molecules derived from primary metabolism (e. g., PUAs in diatoms, dimethylsulfoniopropionate (DMSP) in prymnesiophytes). Producing cells do not seem to suffer physiological impact due to their synthesis. Functional genome sequence data and gene expression analysis will provide insights into regulatory and metabolic pathways in producer organisms, as well as identification of mechanisms of action in target organisms. Understanding chemical ecological responses to environmental triggers and chemically-mediated species interactions will help define crucial chemical and molecular processes that help maintain biodiversity and ecosystem functionality.

The national water quality monitoring in the Lithuanian Baltic Sea waters has started fifty years ago. Consistently implemented long-term monitoring programs are critical for detecting changes in water environment in frame of rapidly changing climate and increasing anthropogenic activity on costal waters. Nevertheless, conventional sampling methods cannot produce enough data about spatial and temporal distribution of phytoplankton blooms, outflow hypertrophic waters of the Curonian Lagoon in the Sea. Satellite based remote sensing provides critical ecological information on global, regional and local scales. However, before the direct use of satellite products for the monitoring and scientific applications, Earth observation data should be validated with in situ measurements for the particular research area.