Institute of Hydrobiology, Biology Centre, Academy of Sciences of the Czech Republic

Environmental exposure to active pharmaceutical ingredients (APIs) can have negative effects on the health of ecosystems and humans. While numerous studies have monitored APIs in rivers, these employ different analytical methods, measure different APIs, and have ignored many of the countries of the world. This makes it difficult to quantify the scale of the problem from a global perspective. Furthermore, comparison of the existing data, generated for different studies/regions/continents, is challenging due to the vast differences between the analytical methodologies employed. Here, we present a global-scale study of API pollution in 258 of the world's rivers, representing the environmental influence of 471.4 million people across 137 geographic regions. Samples were obtained from 1,052 locations in 104 countries (representing all continents and 36 countries not previously studied for API contamination) and analyzed for 61 APIs. Highest cumulative API concentrations were observed in sub-Saharan Africa, south Asia, and South America. The most contaminated sites were in low- to middle-income countries and were associated with areas with poor wastewater and waste management infrastructure and pharmaceutical manufacturing. The most frequently detected APIs were carbamazepine, metformin, and caffeine (a compound also arising from lifestyle use), which were detected at over half of the sites monitored. Concentrations of at least one API at 25.7% of the sampling sites were greater than concentrations considered safe for aquatic organisms, or which are of concern in terms of selection for antimicrobial resistance. Therefore, pharmaceutical pollution poses a global threat to environmental and human health, as well as to delivery of the United Nations Sustainable Development Goals.

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences.

RATIONALE: Airway remodeling in asthma is associated with the accumulation of fibroblasts, the primary cell responsible for synthesis and secretion of extracellular matrix proteins. The process by which the number of fibroblasts increases in asthma is poorly understood, but epithelial-mesenchymal transition (EMT) may play a significant role. OBJECTIVES: To evaluate whether EMT occurs in primary airway epithelial cells (AECs), the mechanisms involved, and if this process is altered in asthmatic AECs. METHODS: AECs were obtained from subjects with asthma (n = 8) and normal subjects without asthma (n = 10). Monolayer and air-liquid interface-AEC (ALI-AEC) cultures were treated with transforming growth factor (TGF)-beta1 (10 ng/ml) for 72 hours and assayed for mesenchymal and epithelial markers using quantitative polymerase chain reaction, confocal microscopy, and immunoblot. The involvement of BMP-7, Smad3, and MAPK-mediated signaling were also evaluated. MEASUREMENTS AND MAIN RESULTS: TGF-beta1-induced EMT in AEC monolayers derived from subjects with asthma and normal donors. EMT was characterized by changes in cell morphology, increased expression of mesenchymal markers EDA-fibronectin, vimentin, alpha-smooth muscle actin, and collagen-1, and loss of epithelial markers E-cadherin and zonular occludin-1. Inhibition of TGF-beta1-induced signaling with Smad3-inhibiting siRNA or TGF-beta1-neutralizing antibodies prevented and reversed EMT, respectively, whereas BMP-7 had no effect. In ALI-AEC cultures derived from normal subjects, EMT was confined to basally situated cells, whereas in asthmatic ALI-AEC cultures EMT was widespread throughout the epithelium. CONCLUSIONS: TGF-beta1 induces EMT in a Smad3-dependent manner in primary AECs. However, in asthmatic-derived ALI-AEC cultures, the number of cells undergoing EMT is greater. These findings support the hypothesis that epithelial repair in asthmatic airways is dysregulated.

In this overview (introductory article to a special issue including 14 papers), we consider all main types of natural and artificial inland freshwater habitas (fwh). For each type, we identify the main biodiversity patterns and ecological features, human impacts on the system and environmental issues, and discuss ways to use this information to improve stewardship. Examples of selected key biodiversity/ecological features (habitat type): narrow endemics, sensitive (groundwater and GDEs); crenobionts, LIHRes (springs); unidirectional flow, nutrient spiraling (streams); naturally turbid, floodplains, large-bodied species (large rivers); depth-variation in benthic communities (lakes); endemism and diversity (ancient lakes); threatened, sensitive species (oxbow lakes, SWE); diverse, reduced littoral (reservoirs); cold-adapted species (Boreal and Arctic fwh); endemism, depauperate (Antarctic fwh); flood pulse, intermittent wetlands, biggest river basins (tropical fwh); variable hydrologic regime—periods of drying, flash floods (arid-climate fwh). Selected impacts: eutrophication and other pollution, hydrologic modifications, overexploitation, habitat destruction, invasive species, salinization. Climate change is a threat multiplier, and it is important to quantify resistance, resilience, and recovery to assess the strategic role of the different types of freshwater ecosystems and their value for biodiversity conservation. Effective conservation solutions are dependent on an understanding of connectivity between different freshwater ecosystems (including related terrestrial, coastal and marine systems).

The heterocytous cyanobacteria form a monophyletic group according to 16S rRNA gene sequence data. Within this group, phylogenetic and morphological studies have shown that genera such as Anabaena and Aphanizomenon are intermixed. Moreover, the phylogeny of the genus Trichormus, which was recently separated from Anabaena, has not been investigated. The aim was to study the taxonomy of the genera Anabaena, Aphanizomenon, Nostoc and Trichormus belonging to the family Nostocaceae (subsection IV.I) by morphological and phylogenetic analyses of 16S rRNA gene, rpoB and rbcLX sequences. New strains were isolated to avoid identification problems caused by morphological changes of strains during cultivation. Morphological and phylogenetic data showed that benthic and planktic Anabaena strains were intermixed. In addition, the present study confirmed that Anabaena and Aphanizomenon strains were not monophyletic, as previously demonstrated. The evolutionary distances between the strains indicated that the planktic Anabaena and Aphanizomenon strains as well as five benthic Anabaena strains in cluster 1 could be assigned to a single genus. On the basis of the 16S rRNA, rpoB and rbcLX gene sequences, the Anabaena/Aphanizomenon strains (cluster 1) were divided into nine supported subclusters which could also be separated morphologically, and which therefore might represent different species. Trichormus strains were morphologically and phylogenetically heterogeneous and did not form a monophyletic cluster. These Trichormus strains, which were representatives of three distinct species, might actually belong to three genera according to the evolutionary distances. Nostoc strains were also heterogeneous and seemed to form a monophyletic cluster, which may contain more than one genus. It was found that certain morphological features were stable and could be used to separate different phylogenetic clusters. For example, the width and the length of akinetes were useful features for classification of the Anabaena/Aphanizomenon strains in cluster 1. This morphological and phylogenetic study with fresh isolates showed that the current classification of these anabaenoid genera needs to be revised.

How many dimensions (trait-axes) are required to predict whether two species interact? This unanswered question originated with the idea of ecological niches, and yet bears relevance today for understanding what determines network structure. Here, we analyse a set of 200 ecological networks, including food webs, antagonistic and mutualistic networks, and find that the number of dimensions needed to completely explain all interactions is small ( < 10), with model selection favouring less than five. Using 18 high-quality webs including several species traits, we identify which traits contribute the most to explaining network structure. We show that accounting for a few traits dramatically improves our understanding of the structure of ecological networks. Matching traits for resources and consumers, for example, fruit size and bill gape, are the most successful combinations. These results link ecologically important species attributes to large-scale community structure.

Biological invasions are responsible for tremendous impacts globally, including huge economic losses and management expenditures. Efficiently mitigating this major driver of global change requires the improvement of public awareness and policy regarding its substantial impacts on our socio-ecosystems. One option to contribute to this overall objective is to inform people on the economic costs linked to these impacts; however, until now, a reliable synthesis of invasion costs has never been produced at a global scale. Here, we introduce InvaCost as the most up-to-date, comprehensive, harmonised and robust compilation and description of economic cost estimates associated with biological invasions worldwide. We have developed a systematic, standardised methodology to collect information from peer-reviewed articles and grey literature, while ensuring data validity and method repeatability for further transparent inputs. Our manuscript presents the methodology and tools used to build and populate this living and publicly available database. InvaCost provides an essential basis (2419 cost estimates currently compiled) for worldwide research, management efforts and, ultimately, for data-driven and evidence-based policymaking.

Malachite green has been used as an effective compound to control external fungal and protozoan infections of fish since 1933 but it has never been registered as a veterinary drug for use in food fish because of its potential carcinogenicity, mutagenicity and teratogenicity in mammals. The present paper reviews negative side-effects of malachite green including its accumulation and persistence in fish that have been treated and describes other alternative substances for the treatment of fish and fish eggs.

Abstract. Water quality data for 56 long-term monitoring sites in eight European countries are used to assess freshwater responses to reductions in acid deposition at a large spatial scale. In a consistent analysis of trends from 1980 onwards, the majority of surface waters (38 of 56) showed significant (p ≤0.05) decreasing trends in pollution-derived sulphate. Only two sites showed a significant increase. Nitrate, on the other hand, had a much weaker and more varied pattern, with no significant trend at 35 of 56 sites, decreases at some sites in Scandinavia and Central Europe, and increases at some sites in Italy and the UK. The general reduction in surface water acid anion concentrations has led to increases in acid neutralising capacity (significant at 27 of 56 sites) but has also been offset in part by decreases in base cations, particularly calcium (significant at 26 of 56 sites), indicating that much of the improvement in runoff quality to date has been the result of decreasing ionic strength. Increases in acid neutralising capacity have been accompanied by increases in pH and decreases in aluminium, although fewer trends were significant (pH 19 of 56, aluminium 13 of 53). Increases in pH appear to have been limited in some areas by rising concentrations of organic acids. Within a general trend towards recovery, some inter-regional variation is evident, with recovery strongest in the Czech Republic and Slovakia, moderate in Scandinavia and the United Kingdom, and apparently weakest in Germany. Keywords: acidification, recovery, European trends, sulphate, nitrate, acid neutralising capacity

In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short-term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well-developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short- and long-term. We summarize the current understanding of storm-induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions.

Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2-1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the 'Black Queen' hypothesis). Genome analyses, moreover, revealed a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria ('Candidatus Nanopelagicales') with two new genera ('Candidatus Nanopelagicus' and 'Candidatus Planktophila') and nine new species.

We have quantified the bacteria, heterotrophic nanoplankton (HNAN), and other microorganisms in 108 lakes, ponds, rivers, and bogs worldwide. These water bodies span the range of biological productivities in freshwater. Numbers of HNAN and bacteria are correlated over four orders of magnitude in each (3 × 10 2 to 4 × 10 6 ml −1 and 3 × 10 5 to 1 × 10 9 ml −1 , respectively) and both increase with the productivity of the water body. Most HNAN are small (2– 5 µ m), colorless, flagellated protists. They grow at about the same rate as bacteria ( µ = 0.01–0.02 h −1 ) and are capable of consuming the entire bacterial production. We suggest that bacterial abundances are regulated by substrate supply and HNAN grazing pressure. Ciliates and other grazing microzooplankton probably limit HNAN abundance, especially in the more productive water bodies. The structure and function of microbial food webs in freshwater environments may thus be similar to those suggested for marine systems.

SYNOPSIS. North America's Great Lakes have recently been invaded by two genetically and morphologically distinct species of Dreissena. The zebra mussel (Dreissena polymorpha) became established in Lake St. Clair of the Laurentian Great Lakes in 1986 and spread throughout eastern North America. The second dreissenid, termed the quagga mussel, has been identified as Dreissena bugensis Andrusov, 1897. The quagga occurs in the Dnieper River drainage of Ukraine and now in the lower Great Lakes of North America. In the Dnieper River, populations of D. polymorpha have been largely replaced by D. bugensis; anecdotal evidence indicates that similar trends may be occurring in the lower Laurentian Great Lakes. Dreissena bugensis occurs as deep as 130 m in the Great Lakes, but in Ukraine is known from only 0–28 m. Dreissena bugensis is more abundant than D. polymorpha in deeper waters in Dneiper River reservoirs. The conclusion that North American quagga mussels have a lower thermal maximum than zebra mussels is not supported by observations made of populations in Ukraine. In the Dnieper River drainage, quagga mussels are less tolerant of salinity than zebra mussels, yet both dreissenids have acclimated to salinities higher than North American populations; eventual colonization into estuarine and coastal areas of North America cannot be ignored.

Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In this study, the rising number of genomic sequences of cyanobacteria and well-described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.

Nitrite is an intermediate in the oxidation of ammonium to nitrate. An elevated ambient nitrite concentration is a potential problem for freshwater fish since nitrite is actively taken up across the gills in competition with chloride. Nitrite is a well-known toxicant for fish as well as a disrupter of multiple physiological functions including ion regulatory, respiratory, cardiovascular, endocrine and excretory processes. One critical consequence of nitrite accumulation is the oxidation of haemoglobin to methaemoglobin, compromising blood oxygen transport. Nitrite toxicity to fish varies considerably and depends on a large number of external and internal factors. Among the most important ones are water quality (e.g. pH, temperature, cation, anion and oxygen concentration), length of exposure, fish species, fish size and age, and individual fish susceptibility. Chloride concentration in water is considered one of the most important factors influencing nitrite toxicity to fish. The importance of individual factors is assessed and re-evaluated continuously.

In late summer 1993 an intensive study was carried out on protozoan grazing in the epilimnion and metalimnion of the eutrophic Rímov Reservoir in south Bohemia. On average, ∼ 70% of bacterial production was consumed by heterotrophic flagellates and 20% by ciliates. Ciliate numbers increased from 5 to 70 cells ml −1 over the 5‐week study period. Ciliates &lt;30 µ m in size were numerically dominant in both layers and included Halteria grandinella and Strobilidium hexakinetum (Oligotrichida), Cyrtolophosis mucicola (Cyrtolophosida), Cinetochilum margaritaceum (Scuticociliatida), Urotricha spp., and Coleps sp. (Prostomatida). Ciliate species‐specific grazing rates on bacteria and picocyanobacteria were determined. The highest individual cell grazing rates, 4,200 bacteria and 560 picocyanobacteria cell −1 h −1 , were observed in Vorticella aquadulcis ‐complex. Oligotrichs ingested on average 360–2,130 bacteria and 76–210 picocyanobacteria cell −1 h −1 , with H. grandinella (1,560 bacteria cell −1 h −1 ), due to its high abundance, as the most important ciliate bacterivore within the system. C. mucicola ingested on average 173 bacteria and 27 cyanobacteria cell −1 h −1 ; C. margaritaceum, 57 bacteria and 7 picocyanobacteria cell −1 h −1 ; and prostomatids, 23–100 bacteria and 2–14 picocyanobacteria cell −1 h −1 . Although there was a tight relationship between grazing rates on bacteria and picocyanobacteria ( r = 0.89, n = 12, P &lt; 0.001), most of the ciliate species preferred larger picoplankton (i.e. picocyanobacteria), as indicated by their clearance rates. According to our data, several oligotrichous ciliate species and Cyclidium sp. can grow in pelagic conditions and exclusively on picoplankton food at rates of one doubling every 24–75 h.

Digital data are accumulating at unprecedented rates. These contain a lot of information about the natural world, some of which can be used to answer key ecological questions. Here, we introduce iEcology (i.e., internet ecology), an emerging research approach that uses diverse online data sources and methods to generate insights about species distribution over space and time, interactions and dynamics of organisms and their environment, and anthropogenic impacts. We review iEcology data sources and methods, and provide examples of potential research applications. We also outline approaches to reduce potential biases and improve reliability and applicability. As technologies and expertise improve, and costs diminish, iEcology will become an increasingly important means to gain novel insights into the natural world.

Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.

Abstract The Baltic Sea is a large brackish semienclosed sea whose species‐poor fish community supports important commercial and recreational fisheries. Both the fish species and the fisheries are strongly affected by climate variations. These climatic effects and the underlying mechanisms are briefly reviewed. We then use recent regional – scale climate – ocean modelling results to consider how climate change during this century will affect the fish community of the Baltic and fisheries management. Expected climate changes in northern Europe will likely affect both the temperature and salinity of the Baltic, causing it to become warmer and fresher. As an estuarine ecosystem with large horizontal and vertical salinity gradients, biodiversity will be particularly sensitive to changes in salinity which can be expected as a consequence of altered precipitation patterns. Marine‐tolerant species will be disadvantaged and their distributions will partially contract from the Baltic Sea; habitats of freshwater species will likely expand. Although some new species can be expected to immigrate because of an expected increase in sea temperature, only a few of these species will be able to successfully colonize the Baltic because of its low salinity. Fishing fleets which presently target marine species (e.g. cod, herring, sprat, plaice, sole) in the Baltic will likely have to relocate to more marine areas or switch to other species which tolerate decreasing salinities. Fishery management thresholds that trigger reductions in fishing quotas or fishery closures to conserve local populations (e.g. cod, salmon) will have to be reassessed as the ecological basis on which existing thresholds have been established changes, and new thresholds will have to be developed for immigrant species. The Baltic situation illustrates some of the uncertainties and complexities associated with forecasting how fish populations, communities and industries dependent on an estuarine ecosystem might respond to future climate change.