Pigment-based chemotaxonomy and CHEMTAX software have proven to be a valuable phytoplankton monitoring tool in marine environments, but are yet underdeveloped to determine algal assemblages in freshwater ecosystems. The main objectives of this study were (1) to compare the results of direct microscopy and CHEMTAX in describing phytoplankton community composition dynamics in a large, shallow and eutrophic lake; (2) to analyze the efficiency of the pigment-based method to detect changes in phytoplankton seasonal dynamics and during rapid bloom periods; (3) to assess the suitability of specific marker pigments and available marker pigment:chlorophyll a ratios to follow seasonal changes in eutrophic freshwater environment. A 5-year (2009-2013) parallel phytoplankton assessment by direct microscopy and by CHEMTAX was conducted using published marker pigment:chlorophyll a ratios. Despite displaying some differences from microscopy results, the pigment-based method successfully described the overall pattern of phytoplankton community dynamics during seasonal cycle in a eutrophic lake. Good agreement between the methods was achieved for most phytoplankton groups - cyanobacteria, chlorophytes, diatoms and cryptophytes. The agreement was poor in case of chrysophytes and dinoflagellates. Our study shows clearly that published marker pigment:chlorophyll a ratios can be used to describe algal class abundances, but they need to be calibrated for specific freshwater environment. Broader use of this method would enable to expand monitoring networks and increase measurement frequencies of freshwater ecosystems to meet the goals of the Water Framework Directive.

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Global warming, paired with eutrophication processes, is shifting phytoplankton communities towards the dominance of bloom-forming and potentially toxic cyanobacteria. The ecosystems of shallow lakes are especially vulnerable to these changes. Traditional monitoring via microscopy is not able to quantify the dynamics of toxin-producing cyanobacteria on a proper spatio-temporal scale. Molecular tools are highly sensitive and can be useful as an early warning tool for lake managers. We quantified the potential microcystin (MC) producers in Lake Peipsi using microscopy and quantitative polymerase chain reaction (qPCR) and analysed the relationship between the abundance of the mcyE genes, MC concentration, MC variants and toxin quota per mcyE gene. We also linked environmental factors to the cyanobacteria community composition. In Lake Peipsi, we found rather moderate MC concentrations, but microcystins and microcystin-producing cyanobacteria were widespread across the lake. Nitrate (NO3−) was a main driver behind the cyanobacterial community at the beginning of the growing season, while in late summer it was primarily associated with the soluble reactive phosphorus (SRP) concentration. A positive relationship was found between the MC quota per mcyE gene and water temperature. The most abundant variant—MC-RR—was associated with MC quota per mcyE gene, while other MC variants did not show any significant impact.

We analysed long-term (1992–2020) changes in fertiliser use, wastewater treatment, and river water nutrient status in Estonia (N-E Europe) in the context of changing socio-economic situations and legislation. We hypothesised that more precise regulation of fertiliser usage and improved wastewater treatment are reflected as declining riverine nutrient concentrations, and that the largest relative improvements occurred in catchments with initially high proportions of point source loading. We used data on population and livestock densities, fertiliser use, and wastewater treatment from the Statistics Estonia database and riverine nutrient concentrations from the environmental monitoring database. We clustered the rivers by their catchment properties and analysed trends and step changes in their nutrient status. Point source nutrient loading reductions explained most of the observed decline in riverine nitrogen and phosphorus concentrations, whereas the application of mineral fertilisers has increased, hindering efforts to reach water quality and nutrient load targets set by the EU Water Framework Directive and the Baltic Sea Action Plan. Highest nitrogen concentrations and strongest increasing trends were found in rivers within the nitrate vulnerable zone, indicating violation of the EU Nitrates Directive. To comply with these directives, resource managers must address non-point source nutrient loading from river watersheds.

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