Effects of multiple stressors on the distribution of fish communities in 203 headwater streams of Rhine, Elbe and Danube

Linking wastewater treatment plant effluents to water quality and hydrology: Effects of multiple stressors on fish communities

Wastewater treatment plants (WWTPs) are essential for maintaining a good water quality of surface waters. However, WWTPs are also associated with water quality deterioration and hydro-morphological alteration. Riverine communities respond to these stressors with changes in their community structure, abundance and diversity. In this study, we used a dataset of 94 monitoring sites across North Rhine-Westphalia, Germany to investigate the influence of WWTPs on the water quality and hydro-morphological quality in river sections downstream of WWTP effluents. More specifically, we analyzed the effects of the percentage of WWTP effluents (in relation to median base flow) on four stressor groups (physico-chemistry, micropollutants, hydrological and morphological alteration) using Linear Mixed Models (LMM). Furthermore, we assessed the impact of a selection of twelve ecologically relevant stressor variables reflecting water quality deterioration and hydro-morphological alteration on reference fish communities using Canonical Correspondence Analysis (CCA). The percentage of WWTP effluents was correlated with water quality, especially with toxic units of a wide range of pharmaceuticals including diclofenac, venlafaxine and sulfamethoxazole (R² up to 0.54) as well as specific pesticides (e.g., terbutryn: R² = 0.33). The correlation of percent WWTP effluents with hydro-morphological alteration was weaker and most pronounced for the frequency of high flow (R² = 0.24) and flow variability (R² = 0.19). About 40 % of the variance in the fish community structure were explained by 12 stressor variables in the CCA models. Water quality and hydrological, but not morphological stressors showed strong albeit highly variable effects on individual fish species. The results indicate that water quality degradation and hydrological alteration are important factors determining the ecological status of fish communities. In this context, WWTP effluents can impose relevant point sources of pollution that affect water quality but also cause alterations of the hydrological regime. Further management measures addressing both stressor groups are needed to improve the ecological status.

A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus

Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.

Multiple environmental stressors affect predation pressure in a tropical freshwater system

Environmental change can alter predator-prey dynamics. However, studying predators in the context of co-occurring environmental stressors remains rare, especially under field conditions. Using in situ filming, we examined how multiple stressors, including temperature and turbidity, impact the distribution and behaviour of wild fish predators of Trinidadian guppies (Poecilia reticulata). The measured environmental variables accounted for 17.6% of variance in predator species composition. While predator species differed in their associations with environmental variables, the overall prevalence of predators was greatest in slow flowing, deeper, warmer and less turbid habitats. Moreover, these warmer and less turbid habitats were associated with earlier visits to the prey stimulus by predators, and more frequent predator visits and attacks. Our findings highlight the need to consider ecological complexity, such as co-occurring stressors, to better understand how environmental change affects predator-prey interactions.

Diurnal patterns of spatial stream temperature variations reveal the need for integrating thermal heterogeneity in riverscape habitat restoration

Longer durations of warmer weather, altered precipitation, and modified streamflow patterns driven by climate change are expected to impair ecosystem resilience, exposing freshwater ecosystems and their biota to a severe threat worldwide. Understanding the spatio-temporal temperature variations and the processes governing thermal heterogeneity within the riverscape are essential to inform water management and climate adaptation strategies. We combined UAS-based imagery data of aquatic habitats with meteorological, hydraulic, river morphology and water quality data to investigate how key factors influence spatio-temporal stream heterogeneity on a diurnal basis within different thermal regions of a large recently restored Danube floodplain. Diurnal temperature ranges of aquatic habitats were larger than expected and ranged between 14.2 and 28.0 °C (mean = 20.7 °C), with peak median temperatures (26.1 °C) around 16:00 h. The observed temperature differences in timing and amplitude among thermal regions were unexpectedly high and created a mosaic pattern of temperature heterogeneity. For example, cooler groundwater-influenced thermal regions provided several cold water patches (CWP, below 19.0 °C) and potential cold water refuges (CWRs) around 12:00 h, at the time when other habitats were warmer than 21.0 °C, exceeding the ecological threshold (20.0 °C) for key aquatic species. Within the morphological complexity of the restored floodplain, we identified groundwater influence, shading and river morphology as the key processes driving thermal riverscape heterogeneity. Promoting stream thermal refuges will become increasingly relevant under climate change scenarios, and river restoration should consider both measures to physically prevent habitat from excessive warming and measures to improve connectivity that meet the temperature requirements of target species for conservation. This requires restoring mosaics of complex and dynamic temperature riverscapes.

Cross-continental evaluation of landscape-scale drivers and their impacts to fluvial fishes: Understanding frequency and severity to improve fish conservation in Europe and the United States

Fluvial fishes are threatened globally from intensive human landscape stressors degrading aquatic ecosystems. However, impacts vary regionally, as stressors and natural environmental factors differ between ecoregions and continents. To date, a comparison of fish responses to landscape stressors over continents is lacking, limiting understanding of consistency of impacts and hampering efficiencies in conserving fishes over large regions. This study addresses these shortcomings through a novel, integrative assessment of fluvial fishes throughout Europe and the conterminous United States. Using large-scale datasets, including information on fish assemblages from more than 30,000 locations on both continents, we identified threshold responses of fishes summarized by functional traits to landscape stressors including agriculture, pasture, urban area, road crossings, and human population density. After summarizing stressors by catchment unit (local and network) and constraining analyses by stream size (creeks vs. rivers), we analyzed stressor frequency (number of significant thresholds) and stressor severity (value of identified thresholds) within ecoregions across Europe and the United States. We document hundreds of responses of fish metrics to multi-scale stressors in ecoregions across two continents, providing rich findings to aid in understanding and comparing threats to fishes across the study regions. Collectively, we found that lithophilic species and, as expected, intolerant species are most sensitive to stressors in both continents, while migratory and rheophilic species are similarly strongly affected in the United States. Also, urban land use and human population density were most frequently associated with declines in fish assemblages, underscoring the pervasiveness of these stressors in both continents. This study offers an unprecedented comparison of landscape stressor effects on fluvial fishes in a consistent and comparable manner, supporting conservation of freshwater habitats in both continents and worldwide.

Pro-ecological and conservation activities are not always beneficial to nature: a case study of two lowland streams in Central Europe

Since 1990 and in particular, after the implementation of the Water Frame Directive, many positive effects of pro-ecological projects are evident; unfortunately, examples of adverse effects have also been observed. This study aims to indicate how some ill-considered actions, called "pro-ecological", may lead to habitat degradation and the disappearance of valuable hydrobiont species. Two watercourses, representing the lowland gravel stream and sandy stream type, were selected for the study. Literature indicated that in the past, these watercourses were characterized by an excellent ecological status and the presence of valuable rheophilic fauna and flora. Environmental parameters were recorded, macroinvertebrates and ichthyofauna were sampled and analyzed, and finally, indexes were calculated. The results were compared with literature data. In the course of studies conducted in 2011-2015, drastic habitat deterioration and extensive changes in the species structure of ichthyofauna and aquatic invertebrates were observed. Changes in the Smolnica stream have been caused by the three retention basins constructed in 2000, along the lower and middle course; while in Kiszewko, however, the factor for habitat deterioration was connected with the excessive expansion of the Eurasian beaver (Castor fiber), which created a beaver pond 20 m in width, with impoundment elevations of up to 2 m.

Spatially structured freshwater fish population dynamics at the River Basin District scale: Implication for environmental management and fish conservation

European Union environmental policy has created a unique regulatory framework to favour aquatic ecosystem management and biodiversity conservation across European countries. Identifying the spatial structure of freshwater fish population dynamics is crucial to define region-specific management and conservation planning. To implement evidence-driven management and conservation decisions at a regional scale we assessed spatial heterogeneity in common freshwater fish population dynamics in France with a focus on trends in River Basin Districts (RBDs). The abundance and biomass growth rates of 18 common European freshwater fish species were estimated with state-space models on 546 sites distributed across the 5 main RBDs sampled in France between 1990 and 2011. Anguilla anguilla, Rutilus rutilus, Salmo trutta fario and Esox spp. exhibited large scale decline in abundance and/or biomass in several RBDs. The other species showed spatial heterogeneity in population growth rates. The main declines were observed in the Adour-Garonne and Loire-Bretagne RBDs, where management and conservation measures are urgently needed to halt the erosion of freshwater fish populations. In each of the 5 investigated RBDs, our results highlight areas where most of the common species we studied exhibited negative population growth rates. Freshwater fish surveys provide the fundamental information necessary to inform the European environmental policies and local environmental management needed to restore freshwater biodiversity. The next steps are to identify the main drivers of freshwater biodiversity erosion in the areas where we demonstrated major declines and to define the most cost-effective restoration measures.

Influence of climate change and extreme weather events on an estuarine fish community

Extreme weather events are becoming more frequent as a result of climate change, and the increasing frequency of these events may lead to significant changes in fish assemblages. In this sense, this work aimed to study the effects of climate change and extreme weather events on fish assemblages in the Rio Minho estuary (Portugal). Between 2010 and 2019, continuous weekly sampling with fyke nets was carried out to assess the dynamics of fish assemblages in the estuary. In addition, temperature and precipitation data were obtained from satellite information to assess the relationship between climatic variables and fish composition, structure, and diversity. Fish populations changed significantly over time, becoming less diverse and largely dominated by a few, mostly invasive species (e.g., carp, goldfish, pumpkinseed, and tench), while the abundance of most native species declined over the years (e.g., panjorca, stickleback, and shad). High temperatures and low precipitation negatively affected native species, while the invasive species benefited from increased temperatures and extreme weather events (droughts and floods).

A first attempt at a holistic analysis of various influencing factors on the fish fauna in the Eastern European Alps

Fish are some of the most threatened vertebrates in the world due to their often-sensitive response to environmental changes. Major land-use changes in the European Alps have direct and indirect impacts on fish communities, and these impacts are expected to increase in the future. Therefore, the identification of factors that are associated with the distribution of fish communities is of great importance to develop guidelines for management, precautions and sustainable use of running waters. In this study, the relationship of various factors - landscape structure and land use, topography, morphology, hydrology, physical and chemical water characteristics, hormonally active substances, pesticides, food availability, fisheries and piscivores birds - with fish assemblages are analysed. Field data from 81 stream sections from 2001 metres above sea level (m.a.s.l.) down to 219 m.a.s.l. are used in the study. The results reveal that the number of fish species has a strong association with topographic characteristics in the catchment area as well as with landscape configuration. Fish abundance and biomass are associated mostly with land-use type, hydrology, morphology as well as topography. In addition, there are indirect connections between fish abundance and biomass through land-use type, topography, water properties and hydromorphology. The results clearly indicate that not a single factor, but a multitude of factors are associated with the fish communities in the Eastern European Alps.

Assessing remote sensing as a tool to monitor hydrological stress in Irish catchments with Freshwater Pearl Mussel populations

The West Coast of Ireland hosts many of the few populations of Freshwater Peal Mussels (FPM) left in Europe. The decline of this keystone species is strongly related to deteriorating hydrological conditions, specifically to the threat of low flows during dry summers. Populations still capable of reproducing require a minimum discharge and flow velocity to support juvenile mussels, or else stress builds up and an entire generation may be lost. Monitoring environmental and hydrological conditions in small and remote FPM catchments is difficult due to the lack of infrastructure. Indices derived from remote sensing imagery can be used to assess hydrological variables at the catchment scale. Here, five indices are tested as possible surrogates for soil moisture and evapotranspiration, based on two relevant land-cover types: open peat habitats (OPH) and forestry. Selected indices are then assessed in their ability to reproduce seasonal patterns and in their response to a severe drought event. The moisture stress index (MSI) and normalized difference vegetation index (NDVI) were found to be the best surrogates for soil moisture and evapotranspiration respectively. Both indices showed seasonality patterns in the two land-cover types, although the variability of MSI was significantly higher. During the 2018 drought, MSI visibly increased only in OPH, while NDVI rose only for forestry. The results suggest that OPH enhances the long-term hydrological resilience of a catchment by conserving water in the peat substrate, while industrial forestry plantations exacerbate the pressure on water during drier periods. This has consequences for river discharge, freshwater biodiversity and specifically for FPM. Implementing these surrogates have the potential to identify land-use management strategies that reduce and even avert the effects of drought on FPM. Such strategies are increasingly necessary in a climate change context, as recurring summer droughts are expected in most of Europe.

Short-Term Effects of Low-Head Barrier Removals on Fish Communities and Habitats

Barrier removal is increasingly being seen as the optimal solution to restore lotic habitat and fish communities, however, evidence of its efficacy is often limited to single sites or catchments. This study used a before–after methodology to examine the short-term (average, 541 days) effects of low-head (0.1–2.9 m) barrier removal at 22 sites distributed across Denmark and northern England on fish density, community, and river habitat responses. Following barrier removal, changes in the aquatic habitat were observed, such that the area immediately upstream of the former barrier location became shallower, with larger substrate and faster flow conditions. The reinstatement of this habitat was especially valuable in Danish streams, where these habitat features are rare, due to the naturally low gradients. Across all 22 sites fish species richness and diversity was similar before and after removal of barriers, likely because of the short study timescale (1–2 years). Across all sites combined, there was an increase in total fish density following barrier removal. A large increase in salmonid (Salmo trutta and Salmo salar) densities following barrier removal occurred at 7 out of 12 Danish sites. No similar response in salmonid density was observed at any of the UK sites which were mostly characterized by high channel gradients and short ponded zones. Two UK barrier removal sites showed marked increases in density of non-salmonid fish species. This study suggests that the removal of low-head barriers can be an effective method of restoring lotic habitats, and can lead to positive changes in fish density in the former ponded zone. The short-term effect of small barrier removal on the fish community is more variable and its effectiveness is likely to be determined by wider riverine processes.

Integrating regional and local monitoring data and assessment tools to evaluate habitat conditions and inform river restoration

Restoring degraded rivers requires initial assessment of the fluvial landscape to identify stressors and riverine features that can be enhanced. We associated local-scale river habitat data collected using standardized national monitoring tools with modeled regional water temperature and flow data on mid-sized northwest U.S. rivers (30-60 m wide). We grouped these rivers according to quartiles of their modeled mean August water temperature and examined their physical habitat structure and flow. We then used principal components analysis to summarize the variation in several dimensions of physical habitat. We also compared local conditions in the Priest River, a river targeted for restoration of native salmonid habitat in northern Idaho, with those in other rivers of the region to infer potential drivers controlling water temperature. The warmest rivers had physical structure and fluvial characteristics typical of thermally degraded rivers, whereas the coldest rivers had higher mean summer flows and greater channel planform complexity. The Priest River sites had approximately twice as many deep residual pools (>50, >75, and >100 cm) and incision that averaged approximately twice that in the coldest rivers. Percentage fines and natural cover in the Priest were also more typical of the higher-temperature river groups. We found generally low instream cover and low levels of large wood both across the region and within the Priest River. Our approach enabled us to consider the local habitat conditions of a river in the context of other similarly sized rivers in the surrounding region. Understanding this context is important for identifying potential influences on river water temperature within the focal basin and for defining attainable goals for management and restoration of thermal and habitat conditions.

Response of European grayling, Thymallus thymallus, to multiple stressors in hydropeaking rivers

Rivers of the large Alpine valleys constitute iconic ecosystems that are highly threatened by multiple anthropogenic stressors. This stressor mix, however, makes it difficult to develop and refine conservation and restoration strategies. It is, therefore, urgent to acquire more detailed knowledge on the consequences and interactions of prevalent stressors on fish populations, in particular, on indicator species such as the European grayling Thymallus thymallus. Here, we conducted a multi-river, multi-stressor investigation to analyze the population status of grayling. Using explorative decision-tree approaches, we disentangled the main and interaction effects of four prevalent stressor groups: flow modification (i.e., hydropeaking), channelization, fragmentation, and water quality alteration. Moreover, using a modified variant of the bootstrapping method, pooled bootstrapping, we determined the optimal number of characteristics that adequately describe fish population status. In our dataset, hydropeaking had the strongest single effect on grayling populations. Grayling biomass at hydrological control sites was around eight times higher than at sites affected by hydropeaking. The primary parameters for predicting population status were downramping rate and peak amplitude, with critical ranges of 0.2-0.4 cm min^-1 and 10-25 cm. In hydropeaking rivers, river morphology and connectivity were the preceding subordinated parameters. Repeating the procedure with pooled bootstrapping datasets strengthened the hypothesis that the identified parameters are most relevant in predicting grayling population status. Hence, hydropeaking mitigation based on ecological thresholds is key to protect and restore already threatened grayling populations. In hydropeaking rivers, high river network connectivity and heterogenous habitat features can dampen the adverse effects of pulsed-flow releases by offering shelter and habitats for all life cycle stages of fish. The presented approach of explorative tree analysis followed by post-hoc tests of identified effects, as well as the pooled bootstrapping method, offers a simple framework for researchers and managers to analyze multi-factorial datasets and draw solid management conclusions.

Land Use Change Influences Ecosystem Function in Headwater Streams of the Lowland Amazon Basin

Intensive agriculture alters headwater streams, but our understanding of its effects is limited in tropical regions where rates of agricultural expansion and intensification are currently greatest. Riparian forest protections are an important conservation tool, but whether they provide adequate protection of stream function in these areas of rapid tropical agricultural development has not been well studied. To address these gaps, we conducted a study in the lowland Brazilian Amazon, an area undergoing rapid cropland expansion, to assess the effects of land use change on organic matter dynamics (OM), ecosystem metabolism, and nutrient concentrations and uptake (nitrate and phosphate) in 11 first order streams draining forested (n = 4) or cropland (n = 7) watersheds with intact riparian forests. We found that streams had similar terrestrial litter inputs, but OM biomass was lower in cropland streams. Gross primary productivity was low and not different between land uses, but ecosystem respiration and net ecosystem production showed greater seasonality in cropland streams. Although we found no difference in stream concentrations of dissolved nutrients, phosphate uptake exceeded nitrate uptake in all streams and was higher in cropland than forested streams. This indicates that streams will be more retentive of phosphorus than nitrogen and that if fertilizer nitrogen reaches streams, it will be exported in stream networks. Overall, we found relatively subtle differences in stream function, indicating that riparian buffers have thus far provided protection against major functional shifts seen in other systems. However, the changes we did observe were linked to watershed scale shifts in hydrology, water temperature, and light availability resulting from watershed deforestation. This has implications for the conservation of tens of thousands of stream kilometers across the expanding Amazon cropland region.

Multiple urban stressors drive fish-based ecological networks in streams of Columbus, Ohio, USA

Integrating a network perspective into multiple-stressor research can reveal indirect stressor effects and simultaneously estimate both taxonomic and functional community characteristics, thus representing a novel approach to stressor paradigms in rivers. Using six years of data from twelve streams of Columbus, Ohio, USA, the effects of nutrients (N:P), impervious surface (%IS), and sedimentation on network properties were quantified. Variability in the strength and distribution of trophic interactions was assessed by incorporating biomass into networks. All stressors impacted some properties of network topology - linkage density (average number of links per species), connectance (fraction of all possible links realized in a network), and compartmentalization (degree to which networks contain discrete sub-webs), including synergistic interactive effects between sedimentation and stream size. We also found support for antagonistic effects between (1) sedimentation and %IS and between %IS and N:P on the weighted index mean link weight, which represents the magnitude of trophic interactions among species in a network, and (2) %IS and stream size on strength standard deviation, a measure of the distribution of total magnitude of all trophic interactions per species in a network. Overall, our results point to the potential for urban stressors such as impervious surfaces and sedimentation - alone and as interactions - to decrease network complexity, compartmentalization, and stability, likely through homogenizing habitat and limiting food resources. The observation that larger streams often buffered the negative effects of these stressors suggests that restoration and other management approaches might be most beneficial in smaller headwater streams of urban catchments.

Assessment of Long-Term Trends in Fish Distributions at Multiple Scales Decreases Uncertainty Associated with Historical Datasets

Monitoring long-term changes in aquatic biodiversity requires the effective use of historical data that were collected with different methods and varying levels of effort. Aggregating data into different spatial scales can control for such differences and provide a robust framework for monitoring distribution trends. We used a quantitative, multi-scale assessment to evaluate the potential drivers of distribution change for 60 fish species at three spatial scales, using 503 unique sampling events conducted between 1931 and 2019 in a stream biodiversity hotspot (French Creek, Pennsylvania, U.S.A). Trends delineated at multiple scales demonstrated that only one cyprinid species consistently declined through time. In contrast, several species, particularly centrarchids (bass and sunfish), appeared to increase with time. However, evidence for species' increases varied among the different spatial scales, and our observations suggest that differences in effort and detection across time periods may contribute to patterns of species increases. There was agreement among scales that agricultural land use, non-native brown trout (Salmo trutta), and anthropogenic barriers did not explain patterns in biodiversity change from the distribution trends in this study. The lack of species declines is likely due to the limited levels of historical impacts in the watershed compared with other locations in the region that experienced more acute pollution bottlenecks. Species increases were most prevalent for sportfish and baitfish species, suggesting that distribution increases were human mediated. Similar multi-scale assessments should provide more robust insight into patterns of biodiversity loss and distribution changes by maximizing the use of historical data.