Long‐term dynamics of phytoplankton have been addressed in marine and lake systems, but rarely in rivers. Large rivers, however, are highly human‐impacted, whereas global warming may further affect the functioning of phytoplankton at long‐term scale. In the middle section of the large European Danube River, long‐term decrease in phytoplankton biomass (Chl‐a) and increase in species diversity have formerly been revealed. The functional community composition that relates to ecosystem functioning directly has not been addressed previously. We analyse a 34‐year‐long phytoplankton data set from the middle river section at Göd (N‐Budapest), Hungary. We focus on gradual changes in the functional composition and functional diversity components based on the functional trait and functional group approaches. We hypothesised that long‐term gradual changes in major environmental constraints should be followed by gradual shifts in dominance relationships among functional traits and functional groups of phytoplankton. We further hypothesised that functional shifts were highlighted by gradual changes in functional diversity components: evenness, divergence and dispersion. Water discharge of the middle Danube shifted towards the more frequent occurrence of lower values. On the other hand, high floods (>3,000 m3/s) increased significantly with shortening tendency in duration and altered seasonality. The concentration of N and P forms, as well as total suspended solids decreased significantly. Water temperature increased significantly, especially in summer. In the phytoplankton, single‐celled eutrophic centric diatoms decreased in relative abundance, but flagellated, elongated and filamentous forms increased. A clear functional shift was the dominance decrease in planktonic taxa and the relative abundance increase in benthic diatoms. All functional diversity components increased significantly in the entire data set, except functional evenness (FEVE) based on the functional group approach. At seasonal scale, all significant trends showed increases, except the FEVE components of the functional group approach, which decreased in winter and spring significantly. Long‐term increase in functional diversity components alone could indicate enhanced ecosystem functioning of phytoplankton in the middle section of the Danube. However, we argue that the observed increase in functional diversity may be related to a gradual shift from high‐biomass communities with the dominance of eutrophic centric diatoms towards the relative increase in several, but low‐biomass elements. These include a few planktonic algae well adapted to the altered conditions, diatoms with benthic origin and dispersed limnophilic taxa. Our results provide the first evidence for a long‐term phytoplankton functional regime shift in a European large river. Global warming, human impacts and oligotrophication might potentially increase the functional diversity of large river phytoplankton, but the origin and functional role of taxa should carefully be considered. The ...

Reduced body size is among the universal ecological responses to global warming. Our knowledge on how altered body size affects ecosystem functioning in ectothermic aquatic organisms is still limited. We analysed trends in the cell size structure of phytoplankton in the middle Danube River over a 34-year period at multiple levels: (1) average cell size of assemblages (ACS), (2) within the centric diatom community and (3) in the dominant centric diatom taxon: Stephanodiscus. We asked whether global warming and human impacts affected the average cell size of phytoplankton. Also, whether the altered size structure affected how chlorophyll-a, as an ecosystem functioning measure, relates to the ACS of phytoplankton. The cell size of phytoplankton decreased significantly at all organisation levels, and the assemblages became more dispersed in cell size over time. Environmental variables related to global warming and human impacts affected the ACS of phytoplankton significantly. The relationship between chlorophyll-a and the ACS of phytoplankton shifted from negative linear to broad and then narrow hump shape over time. Longer water residence time, warming and decline in nutrients and suspended solids decrease the ACS of phytoplankton in the middle Danube and expectedly in other large rivers. Our results suggest that cell size decrease in phytoplankton, especially of centric diatoms, constrains planktic algal biomass production in large rivers, independently of algal density. Such cell size decrease may also affect higher trophic levels and enhance the more frequent occurrence of “clear-water” plankton in large, human-impacted rivers under global change.

Analysis of transcriptional regulatory interactions and their comparisons across multiple species are crucial for progress in various fields in biology, from functional genomics to the evolution of signal transduction pathways. However, despite the rapidly growing body of data on regulatory interactions in several eukaryotes, no databases exist to provide curated high-quality information on transcription factor–target gene interactions for multiple species. Here, we address this gap by introducing the TFLink gateway, which uniquely provides experimentally explored and highly accurate information on transcription factor–target gene interactions (∼12 million), nucleotide sequences and genomic locations of transcription factor binding sites (∼9 million) for human and six model organisms: mouse, rat, zebrafish, fruit fly, worm and yeast by integrating 10 resources. TFLink provides user-friendly access to data on transcription factor–target gene interactions, interactive network visualizations and transcription factor binding sites, with cross-links to several other databases. Besides containing accurate information on transcription factors, with a clear labelling of the type/volume of the experiments (small-scale or high-throughput), the source database and the original publications, TFLink also provides a wealth of standardized regulatory data available for download in multiple formats. The database offers easy access to high-quality data for wet-lab researchers, supplies data for gene set enrichment analyses and facilitates systems biology and comparative gene regulation studies. Database URL https://tflink.net/

(1) Urbanization significantly influences the ecosystems of rivers in various ways, including the so-called loading effect of wastewater production. Benthic diatoms are used in ecological status assessments of waters. Beside species composition, traits can be used as indicators. We aimed to evaluate how the loading of the large city of Budapest manifests in the physico-chemical variables of the River Danube and what species composition and trait response this loading results in for the benthic diatom communities. (2) Weekly samplings were performed at points upstream and downstream of Budapest on both riverbanks. Samples were compared, based on general physical-chemical variables and the concentration of thirty-four elements, as well as species composition and seven traits of species of diatom communities. Ecological status was assessed using the Specific Pollution Sensitivity Index (IPS). (3) Only a few measured environmental variables showed differences between the sampling points, suggesting that the nutrient loading has significantly decreased due to the installation of several efficiently working wastewater treatment plants since the introduction of the European Union Water Framework Directive. In contrast, the species composition and traits of species showed the effect of land use. Benthic diatoms indicate the environmental changes caused by land use in the longer-term, while chemical measurements reflect instantaneous status.

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Here we report the results of our decades-long study on epiphytic communities from two tributary systems of the Szigetköz section of the Danube River. The main goal of the investigation was to detect changes in the epiphytic communities at structural (core species, changes in the relative abundance of common species) and functional (trait changes) levels as a result of the most important anthropogenic effects on Szigetköz, i.e., hydro-morphological modifications. We also examined the impact of rehabilitation on the tributary systems in terms of ecological potential. We discovered that mainly motile diatom species characterized the epiphyton due to reduced water volume were introduced into the tributary system after the diversion of the Danube. The ecosystem stabilized in the rehabilitated section, while the non-rehabilitated section showed a worsening tendency, mainly in the parapotamic branches. Our long-term data sets may provide a good basis for comparisons of different aquatic ecosystems, to define changes in the abundance of core species and in the structure of community in response to different anthropogenic pressures. It is fundamental to determine adaptive traits in assessing the impact of global warming stressors on biodiversity.

Seasonal environmental variation is a leading driver of microbial planktonic community assembly and interactions. Yet, unexpected departures from general seasonal successional trends are often reported. To understand the role of local stochastic events in modifying seasonal succession, we sampled fortnightly throughout three seasons (spring, summer, and autumn) five nearby shallow soda lakes exposed to the same seasonal meteorological changes. We characterised their microeukaryotic and bacterial communities by 18S and 16S rRNA gene sequencing, respectively. Biological interactions were inferred by the analyses of synchronous and time-shifted interaction networks, and the keystone taxa were topologically identified. The pans showed similar succession patterns during the study period with spring being characterised by high relevance of trophic interactions and certain level of community stability followed by a more dynamic and variable summer-autumn period both in respect of community composition and microbial interactions. Adaptation to general seasonal changes happened through the abundant shared core microbiome of the pans. However, stochastic events such as desiccation and cyanobacterial blooms disrupted common network attributes and introduced shifts from the prevalent seasonal trajectory. These were more pronounced for microeukaryotes than for bacteria which was reflected in increased turnover and contribution of non-core microeukaryotes. Our results demonstrated that despite being extreme and highly variable habitats, shallow soda lakes exhibit certain similarities in the seasonality of their planktonic communities, yet random stochastic events such as droughts can instigate substantial deviations from prevalent trends for the microeukaryotic but not bacterial communities.