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2025

Cano-Barbacil, C., Sinclair, J.S., Welti, E.A.R., Haase, P. (2025) Recovery and Degradation Drive Changes in the Dispersal Capacity of Stream Macroinvertebrate Communities. Global Change Biology, 31(1), e70054. https://doi.org/10.1111/gcb.70054

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Freshwater ecosystems face significant threats, including pollution, habitat loss, invasive species, and climate change. To address these challenges, management strategies and restoration efforts have been broadly implemented. Across Europe, such efforts have resulted in overall improvements in freshwater biodiversity, but recovery has stalled or failed to occur in many localities, which may be partly caused by the limited dispersal capacity of many species. Here, we used a comprehensive dataset comprising 1327 time series of freshwater macroinvertebrate communities ranging from 1968 to 2021 across 23 European countries to investigate whether dispersal capacity changes with the ecological quality of riverine systems. Sites experiencing improvements in ecological quality exhibited a net gain in species and tended to have macroinvertebrate communities containing species with stronger dispersal capacity (e.g., active aquatic and aerial dispersers, species with frequent propensity to drift, and insects with larger wings). In contrast, sites experiencing degradation of ecological quality exhibited a net loss of species and a reduction in the proportion of strong dispersers. However, this response varied extensively among countries and local sites, with some improving sites exhibiting no parallel gains in macroinvertebrates with higher dispersal capacity. Dispersal capacity of the local species pool can affect the success of freshwater ecosystem restoration projects. Management strategies should focus on enhancing landscape connectivity to create accessible “source” areas and refugia for sensitive taxa, especially as climate change reshapes habitat suitability. Additionally, biodiversity initiatives must incorporate adaptive decision-making approaches that account for the site-specific responses of macroinvertebrate communities to changes in ecological quality.

Haase, P., Cortés-Guzmán, D., He, F., Jupke, J.F., Mangadze, T., Pelicice, F.M., [. . .], Sinclair, J.S. (2025) Successes and failures of conservation actions to halt global river biodiversity loss. Nature Reviews Biodiversity. https://doi.org/10.1038/s44358-024-00012-x

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To address the losses of river biodiversity worldwide, various conservation actions have been implemented to promote recovery of species and ecosystems. In this Review, we assess the effectiveness of these actions globally and regionally, and identify causes of success and failure. Overall, actions elicit little improvement in river biodiversity, in contrast with reports from terrestrial and marine ecosystems. This lack of improvement does not necessarily indicate a failure of any individual action. Rather, it can be attributed in part to remaining unaddressed stressors driving biodiversity loss; a poor match between the spatial scale of action and the scale of the affected area; and absence of adequate monitoring, including insufficient timescales, missing reference and control sites or insufficient selection of targeted taxa. Furthermore, outcomes are often not reported and are unevenly distributed among actions, regions and organism groups. Expanding from local-scale actions to coordinated, transformative, catchment-scale management approaches shows promise for improving outcomes. Such approaches involve identifying major stressors, appropriate conservation actions and source populations for recolonization, as well as comprehensive monitoring, relevant legislation and engaging all stakeholders to promote the recovery of river biodiversity.


Hesse, T., Niemann, F., Khaliq, S., Koster, D., Enss, J., Feld, C.K., [. . .], Schmidt, T.C. (2025) A Proof-of-Principle Study for delta15N Measurements of Aqueous Dissolved Nitrate With a Modified LC-IRMS Interface. Rapid Communications in Mass Spectrometry, 39(3), e9950. https://doi.org/10.1002/rcm.9950

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2024

Venkataramanan, A., Kloster, M., Burfeid-Castellanos, A., Dani, M., Mayombo, N.A.S., Vidakovic, D., [. . .], Beszteri, B. (2024) "UDE DIATOMS in the Wild 2024": a new image dataset of freshwater diatoms for training deep learning models. Gigascience, 13. https://doi.org/10.1093/gigascience/giae087

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Background

Diatoms are microalgae with finely ornamented microscopic silica shells. Their taxonomic identification by light microscopy is routinely used as part of community ecological research as well as ecological status assessment of aquatic ecosystems, and a need for digitalization of these methods has long been recognized. Alongside their high taxonomic and morphological diversity, several other factors make diatoms highly challenging for deep learning–based identification using light microscopy images. These include (i) an unusually high intraclass variability combined with small between-class differences, (ii) a rather different visual appearance of specimens depending on their orientation on the microscope slide, and (iii) the limited availability of diatom experts for accurate taxonomic annotation.

Findings

We present the largest diatom image dataset thus far, aimed at facilitating the application and benchmarking of innovative deep learning methods to the diatom identification problem on realistic research data, “UDE DIATOMS in the Wild 2024.” The dataset contains 83,570 images of 611 diatom taxa, 101 of which are represented by at least 100 examples and 144 by at least 50 examples each. We showcase this dataset in 2 innovative analyses that address individual aspects of the above challenges using subclustering to deal with visually heterogeneous classes, out-of-distribution sample detection, and semi-supervised learning.

Conclusions

The problem of image-based identification of diatoms is both important for environmental research and challenging from the machine learning perspective. By making available the so far largest image dataset, accompanied by innovative analyses, this contribution will facilitate addressing these points by the scientific community.


Farias, L., Beszteri, B., Burfeid Castellanos, A., Doliwa, A., Enss, J., Feld, C.K., [. . .], Le, T.T.Y. (2024) Influence of salinity on the thermal tolerance of aquatic organisms. Science of the Total Environment, 953, 176120. https://doi.org/10.1016/j.scitotenv.2024.176120

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Aquatic organisms are challenged by changes in their external environment, such as temperature and salinity fluctuations. If these variables interacted with each other, the response of organisms to temperature changes would be modified by salinity and vice versa. We tested for potential interaction between temperature and salinity effects on freshwater, brackish, and marine organisms, including algae, macrophytes, heterotrophic protists, parasites, invertebrates, and fish. We performed a meta-analysis that compared the thermal tolerance (characterised by the temperature optimum, lower and upper temperature limits, and thermal breadth) at various salinities. The meta-analysis was based on 90 articles (algae: 15; heterotrophic protists: 1; invertebrates: 43; and fish: 31). Studies on macrophytes and parasites were lacking. We found that decreasing salinity significantly increased and decreased the lower and upper temperature limits, respectively, in all groups. Thus, a lowered salinity increased the thermal sensitivity of organisms. These findings mainly reflect the response of brackish and marine organisms to salinity changes, which dominated our database. The few studies on freshwater species showed that their lower thermal limits increased and the upper thermal limits decreased with increasing salinity, albeit statistically nonsignificant. Although non-significant, the response of thermal tolerance to salinity changes differed between various organism groups. It generally decreased in the order of: algae > invertebrates > fish. Overall, our findings indicate adverse effects of salinity changes on the temperature tolerance of aquatic organisms. For freshwater species, studies are comparatively scarce and further studies on their thermal performance at various salinity gradients are required to obtain more robust evidence for interactions between salinity and temperature tolerance. Considering test conditions such as acclimation temperature and potential infection with parasites in future studies may decrease the variability in the relationship between salinity and thermal tolerance.


Mayombo, N.A.S., Dani, M., Kloster, M., Vidaković, D., Buchner, D., Burfeid-Castellanos, A.M., Beszteri, B. (2024) Assessment of microphytobenthos communities in the Kinzig catchment using photosynthesis-related traits, digital light microscopy and 18S-V9 amplicon sequencing. Frontiers in Ecology and Evolution, 12. https://doi.org/10.3389/fevo.2024.1422925

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Introduction: Microalgae form an essential group of benthic organisms that respond swiftly to environmental changes. They are widely used as bioindicators of anthropogenic stressors in freshwater ecosystems. We aimed to assess the responses of microalgae communities to multiple environmental stressors in the Kinzig River catchment, home to a long-term ecological monitoring site, in Germany.

Methods: We used a photosynthetic biomass proxy alongside community composition of diatoms assessed by digital light microscopy, and of microalgae by 18S-V9 amplicon sequencing, to characterise microalgae at 19 sampling sites scattered across the catchment.

Results: Our results revealed significant effects of physical and chemical factors on microalgae biomass and community compositions. We found that conductivity, water temperature and pH were the most important factors affecting microalgae community composition, as observed in both microscopy and amplicon analysis. In addition to these three variables, the effect of total phosphate on all microalgae, together with water discharge on the diatom (Bacillariophyta) communities, as assessed by amplicon analysis, may reveal taxon-specific variations in the ecological responses of different microalgal groups.

Discussion: Our results highlighted the complex relationship between various environmental variables and microalgae biomass and community composition. Further investigations, involving the collection of time series data, are required to fully understand the underlying biotic and abiotic parameters that influence these microalgae communities.


Boden, L., Klagus. C., Boenigk, J. (2024) Insights from single-strain and mixed culture experiments on the effects of heatwaves on freshwater flagellates. PeerJ, 12:e17912. http://doi.org/10.7717/peerj.17912

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The increasing frequency and intensity of heatwaves driven by climate change significantly impact microbial communities in freshwater habitats, particularly eukaryotic microorganisms. Heterotrophic nanoflagellates are important bacterivorous grazers and play a crucial role in aquatic food webs, influencing the morphological and taxonomic structure of bacterial communities. This study investigates the responses of three flagellate taxa to heatwave conditions through single-strain and mixed culture experiments, highlighting the impact of both biotic and abiotic factors on functional redundancy between morphologically similar protist species under thermal stress. Our results indicate that temperature can significantly impact growth and community composition. However, density-dependent factors also had a significant impact. In sum, stabilizing effects due to functional redundancy may be pronounced as long as density-dependent factors play a minor role and can be overshadowed when flagellate abundances increase.


Kuppels, A., Bayat, H.S., Gillmann, S.M., Schäfer, R.B., Vos, M. (2024) Putting the Asymmetric Response Concept to the test: modelling multiple stressor exposure and release in a stream food web. Science of the Total Environment, 174722. https://doi.org/10.1016/j.scitotenv.2024.174722

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Communities in stream ecosystems often respond asymmetrically to increase and release of stressors, as indicated by slow and incomplete recovery. The Asymmetric Response Concept (ARC) posits that this is due to a shift in the relative importance of three mechanisms: tolerance, dispersal, and biotic interactions. In complex natural communities, these mechanisms may produce alternative outcomes through poorly understood indirect effects. To understand how the three mechanisms respond to different temporal stressor scenarios, we studied multiple scenarios using a stream food web model. We asked the following questions: Do groups of species decline as expected on the basis of individual tolerance rankings derived from laboratory experiments when they are embedded in a complex dynamic food web?

Does the response of ecosystem function match that of communities? To address these questions, we aggregated data on individual tolerances at the level of functional groups and studied how single and multiple stressors affect food web dynamics and nutrient cycling. Multiple stressor scenarios involved different intensities of salt and temperature increase. Functional groups exhibited a different relative tolerance ranking between the laboratory and dynamic food web contexts. Salt as a single stressor had only minor and transient effects at low level but led to the loss of one or more functional groups at high level. In contrast, high temperature, alone or in combination with salt, caused the loss of functional groups at all tested levels. Patterns often differed between the response of communities and ecosystem function. We discuss our findings with respect to the ARC.


Mayombo, N.A.S., Burfeid-Castellanos, A.M., Vermiert, A.M., Pimentel, I.M., Rehsen, P.M., Dani, M., [. . .], Beszteri, B. (2024) Functional and compositional responses of stream microphytobenthic communities to multiple stressors increase and release in a mesocosm experiment. Science of the Total Environment, 943, 173670. https://doi.org/10.1016/j.scitotenv.2024.173670

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Field observations form the basis of the majority of studies on microphytobenthic algal communities in freshwater ecosystems. Controlled mesocosm experiments data are comparatively uncommon. The few experimental mesocosm studies that have been conducted provide valuable insights into how multiple stressors affect the community structures and photosynthesis-related traits of benthic microalgae. The recovery process after the stressors have subsided, however, has received less attention in mesocosm studies. To close this gap, here we present the results of a riparian mesocosm experiment designed to investigate the effects of reduced flow velocity, increased salinity and increased temperature on microphytobenthic communities. We used a full factorial design with a semi-randomised distribution of treatments consisting of two levels of each stressor (2 × 2 × 2 treatments), with eight replicates making a total of 64 circular mesocosms, allowing a nuanced examination of their individual and combined influences. We aimed to elucidate the responses of microalgae communities seeded from stream water to the applied environmental stressors. Our results showed significant effects of reduced flow velocity and increased temperature on microphytobenthic communities. Recovery after stressor treatment led to a convergence in community composition, with priority effects (hypothesized to reflect competition for substrate between resident and newly arriving immigrant taxa) slowing down community shifts and biomass increase. Our study contributes to the growing body of literature on the ecological dynamics of microphytobenthos and emphasises the importance of rigorous experiments to validate hypotheses. These results encourage further investigation into the nuanced interactions between microphytobenthos and their environment and shed light on the complexity of ecological responses in benthic systems.


Escobar-Sierra, C., Cañedo-Argüelles, M., Vinyoles, D., Lampert, K.P. (2024) Unraveling the molecular mechanisms of fish physiological response to freshwater salinization: A comparative multi-tissue transcriptomic study in a river polluted by potash mining. Environmental Pollution, 357, 124400. https://doi.org/10.1016/j.envpol.2024.124400

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Freshwater salinization is an escalating global environmental issue that threatens freshwater biodiversity, especially fish populations. This study aims to uncover the molecular basis of salinity physiological responses in a non-native minnow species (Phoxinus septimaniae x P. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge) were examined. Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity physiological response in non-native minnows confronting diverse environmental stressors. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish physiological response in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing salinization.


Markert, N., Guhl, B., Feld, C.K. (2024) Linking wastewater treatment plant effluents to water quality and hydrology: Effects of multiple stressors on fish communities. Water Research, 260, 121914. https://doi.org/10.1016/j.watres.2024.121914

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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.


Enss, J., Nachev, M., Jochmann, M.A., Schmidt, T.C., Feld, C.K. (2024) Stable isotopes (15N) facilitate non‐invasive labelling of large quantities of macroinvertebrates across different species and feeding types. Ecology and Evolution, 14(6), e11539. https://doi.org/10.1002/ece3.11539

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While macroinvertebrate dispersal operates at the individual level, predictions of their dispersal capabilities often rely on indirect proxies rather than direct measurements. To gain insight into the dispersal of individual specimens, it is crucial to mark (label) and capture individuals. Isotopic enrichment with 15N is a non-invasive method with the potential of labelling large quantities of macroinvertebrates. While the analysis of 15N is widely utilised in food web studies, knowledge on the specific utility of isotopic enrichment with 15N for mass labelling of macroinvertebrate individuals across different taxa and feeding types is limited.

Previous studies have focused on single species and feeding types, leaving gaps in our understanding of the broader applicability of this method. Therefore, this study aimed to test and compare isotopic mass enrichment across several macroinvertebrate taxa and feeding types. We released 15NH4Cl at five stream reaches in North-Rhine Westphalia, Germany, and successfully enriched 12 distinct macroinvertebrate taxa (Crustacea and Insecta).

Significant enrichment was achieved in active and passive filter feeders, grazers, shredders and predators, and predominantly showed positive correlations with the enrichment of the taxa's main food sources phytobenthos and particulate organic matter. Enrichment levels rose rapidly and peaked at distances between 50 m and 300 m downstream of the isotopic inlet; significant enrichment occurred up to 2000 m downstream of the isotopic inlet in all feeding types. Macroinvertebrate density estimates on the stream bottom averaged to a total of approximately 3.4 million labelled individuals of the 12 investigated taxa, thus showing the high potential of isotopic (15N) enrichment as a non-invasive method applicable for mass labelling across different macroinvertebrate feeding types. Hence, isotopic enrichment can greatly assist the analysis of macroinvertebrate dispersal through mark-and-recapture experiments, as it allows to measure the movement at the level of individual specimens.


David, G.M., Madge Pimentel, I., Rehsen, P.M., Vermiert, A.M., Leese, F., Gessner, M.O. (2024) Multiple stressors affecting microbial decomposer and litter decomposition in restored urban streams: Assessing effects of salinization, increased temperature, and reduced flow velocity in a field mesocosm experiment. Science of the Total Environment, 934, 173669. https://doi.org/10.1016/j.scitotenv.2024.173669

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A multitude of anthropogenic stressors impact biological communities and ecosystem processes in urban streams. Prominent among them are salinization, increased temperature, and altered flow regimes, all of which can affect microbial decomposer communities and litter decomposition, a fundamental ecosystem process in streams. Impairments caused by these stressors individually or in combination and recovery of communities and ecosystem processes after release from these stressors are not well understood. To improve our understanding of multiple stressors impacts we performed an outdoor stream mesocosm experiment with 64 experimental units to assess the response of microbial litter decomposers and decomposition. The three stressors we applied in a full-factorial design were increased salinity (NaCl addition, 0.53 mS cm-1 above ambient), elevated temperature (3.5 °C above ambient), and reduced flow velocity (3.5 vs 14.2 cm s-1). After two weeks of stressor exposure (first sampling) and two subsequent weeks of recovery (second sampling), we determined leaf-associated microbial respiration, fungal biomass, and the sporulation activity and community composition of aquatic hyphomycetes in addition to decomposition rates of black alder (Alnus glutinosa) leaves confined in fine-mesh litter bags. Microbial colonization of the litter was accompanied by significant mass loss in all mesocosms. However, there was little indication that mass loss, microbial respiration, fungal biomass, sporulation rate or community composition of aquatic hyphomycetes was strongly affected by either single stressors or their interactions. Two exceptions were temperature effects on sporulation and decomposition rate. Similarly, no notable differences among mesocosms were observed after the recovery phase. These results suggest that microbial decomposers and leaf litter decomposition are either barely impaired by exposure to the tested stressors at the levels applied in our experiment, or that communities in restored urban streams are well adapted to cope with these stressor levels.


Peters, K., Grantz, S.F., Kiesel, J., Lewandowski, J., Fohrer, N. (2024) Hyporheic exchange flows in a mountainous river catchment identified by distributed temperature sensing. River Research and Applications. https://doi.org/10.1002/rra.4306

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Elevated stream temperatures under low-flows, exacerbated by global warming, are a stressor that affects aquatic species directly or in combination with other stressors. Stream temperatures are influenced by energy fluxes across the air–water interface as well as by hydrological exchange processes occurring at the water–riverbed interface. Small-scale stream temperature dynamics influenced by exchange flows are still underrepresented in stream temperature research. To investigate high-resolution temperature dynamics and hydrological exchange processes at the sediment–water interface we applied fiber-optic distributed temperature sensing (FO-DTS) at two sites in the mountainous Kinzig catchment combined with mapping and measurement of additional environmental conditions. Two types of temperature anomalies could be observed at one site under conditions of low flow and high air temperature. Dampening effects coincided with riverine features such as pools, vegetation roots, fine sediment, and signs of streambank seepage which indicated hyporheic exchange flows. Increased heating of the substrate during the day was identified in shallow sections where sediment was exposed to the air and shading from riparian vegetation was patchy. At another site, at which the cable could not be buried because of the sediment composition, temperature anomalies in the overlying water indicated diffuse groundwater exfiltration. The results show that small-scale processes in the hyporheic zone, low water tables, and riparian shading influence stream temperature in mountainous streams and can be identified with FO-DTS under suitable conditions. The results improve our understanding of stream temperatures (in the hyporheic zone) and provide important information on how to improve hydrological modeling.


Medina Madariaga, G., Ferreira, V., Arora, R., Mansour, I., David, G.M., Jähnig, S.C., He, F. (2024) Multiple‐stressor effects on leaf litter decomposition in freshwater ecosystems: A meta‐analysis. Functional Ecology, 38(7), 1523-1536. https://doi.org/10.1111/1365-2435.14571

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  1. Recent years have witnessed a surge in research on the effects of multiple stressors in freshwater ecosystems. While studies have increased, the synthesis of their findings into a broader understanding of ecosystem-level effects remains an ongoing endeavour. Leaf litter decomposition, a frequently investigated and pivotal ecosystem function in freshwaters, is sensitive to changes in abiotic conditions and biotic communities, and therefore susceptible to multiple-stressor effects.
  2. Here, we synthesize findings from 27 manipulative experimental studies encompassing 61 responses of litter decomposition to paired stressors such as warming, nutrient enrichment and emerging pollutants in freshwater ecosystems. We calculated the individual and overall interaction effect sizes resulting from two stressors occurring simultaneously. Furthermore, we analysed the effect of moderator variables in the size and direction of interaction effect sizes using a meta-analytical approach.
  3. Although the vote-counting method showed additive interactions to dominate individual observations (91.8%), weighted random-effects meta-analysis revealed an overall antagonistic interaction between stressors (i.e. the cumulative effect of paired stressors on litter decomposition was less than the sum of their single effects). Our results emphasized the influence of experimental characteristics such as macroinvertebrate involvement, habitat type (lentic vs. lotic) and litter quality (assumed from plant mycorrhizal association) in shaping the responses of litter decomposition to multiple stressors.
  4. Our meta-analysis highlights the need to incorporate local ecological complexities in manipulative experiments to improve predictions of multiple-stressor effects on biodiversity and ecosystem functions. The present study underscores the importance of considering biotic interactions and adopting the metacommunity framework in conservation and restoration actions to support the management of freshwater ecosystems in an era of rapid global change.

Kaijser, W., Lorenz, A.W., Brauer, V.S., Burfeid Castellanos, A., David, G.M., Nuy, J.K., [. . .], Hering, D. (2024) Differential associations of five riverine organism groups with multiple stressors. Science of the Total Environment, 934, 173105. https://doi.org/10.1016/j.scitotenv.2024.173105

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The decline of river and stream biodiversity results from multiple simultaneous stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish.

Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models.

Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.


Lee, K.S., Landry, Z., Athar, A., Alcolombri, U., Pramoj Na Ayutthaya, P., Berry, D., [. . .], Meckenstock, R., [. . .], Probst, A.J., [. . .], Stocker, R. (2024) MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. Nature Microbiology, 9, 1152–1156 . https://doi.org/10.1038/s41564-024-01656-3

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Here we present the establishment of an open-access web-based repository for microbiological Raman spectroscopy data. The data collection, called ‘MicrobioRaman’ (https://www.ebi.ac.uk/biostudies/MicrobioRaman/studies), was inspired by the great success and usefulness of research databases such as GenBank and UniProt. This centralized repository, residing within the BioStudies database1 — which is maintained by a public institution, the European Bioinformatics Institute — minimizes the risk of data loss or eventual abandonment, offering a long-term common reference for analysis with advantages in accessibility and transparency over commercial data analysis tools. We feel that MicrobioRaman will provide a foundation for this growing field by serving as an open-access repository for sharing microbiological Raman data and through the codification of a set of reporting standards.


Prati, S., Grabner, D.S., Hupało, K., Weiperth, A., Maciaszek, R., Lipták, B., [. . .], Sures, B. (2024) Invisible invaders: range expansion of feral Neocaridina davidi offers new opportunities for generalist intracellular parasites. Biological Invasions. https://doi.org/10.1007/s10530-024-03324-3

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The release of ornamental pets and associated pathogens outside their native range might directly or indirectly impact the recipient community. In temperate regions, e.g., central Europe, feral freshwater species of tropical and sub-tropical origins are mainly constrained to thermally polluted waters and thermal springs. However, species with high environmental plasticity and reproduction rates, such as the shrimp Neocaridina davidi, may adapt to colder water regimes over time. A widening thermal niche may eventually overcome thermal barriers, further expanding the range and enhancing transmission opportunities for host generalist parasites. This study assesses the observed (field observations) and theoretical (species distribution models) range expansion of N. davidi and associated parasites in Europe. We report three newly established N. davidi populations from thermally polluted waters in central Europe (Germany, Hungary, and Slovakia) and provide further evidence of its range expansion into colder environments. Species distribution models predict thermally suitable habitats in the Mediterranean and a foreseeable expansion into Western Europe and the Balkans by 2050. We confirm the presence of the microsporidian parasite Ecytonucleospora hepatopenaei in feral N. davidi populations across Europe and expand the list of microsporidians found in this host from two to four. Furthermore, we provide the first evidence of parasite spillover from/to the invasive crayfish Procambarus clarkii, suggesting that parasite exchange with native biota might be possible. Such possibility, coupled with an ongoing range expansion of N. davidi bolstered by human-mediated introductions and climate change, will likely exacerbate the impact on native biota.


Nguyen, H.H., Peters, K., Kiesel, J., Welti, E.A.R., Gillmann, S.M., Lorenz, A.W., [. . .], Haase, P. (2024) Stream macroinvertebrate communities in restored and impacted catchments respond differently to climate, land-use, and runoff over a decade. Science of the Total Environment, 929, 172659. https://doi.org/10.1016/j.scitotenv.2024.172659

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Identifying which environmental drivers underlie degradation and improvements of ecological communities is a fundamental goal of ecology. Achieving this goal is a challenge due to diverse trends in both environmental conditions and ecological communities across regions, and it is constrained by the lack of long-term parallel monitoring of environmental and community data needed to study causal relationships. Here, we identify key environmental drivers using a high-resolution environmental - ecological dataset, an ensemble of the Soil and Water Assessment Tool (SWAT+) model, and ecological models to investigate effects of climate, land-use, and runoff on the decadal trend (2012−2021) of stream macroinvertebrate communities in a restored urban catchment and an impacted catchment with mixed land-uses in Germany. The decadal trends showed decreased precipitation, increased temperature, and reduced anthropogenic land-uses, which led to opposing runoff trends – with decreased runoff in the restored catchment and increased runoff in the impacted catchment. The two catchments also varied in decadal trends of taxonomic and trait composition and metrics. The most significant improvements over time were recorded in communities of the restored catchment sites, which have become wastewater free since 2007 to 2009. Within the restored catchment sites, community metric trends were primarily explained by land-use and evaporation trends, while community composition trends were mostly associated with precipitation and runoff trends. Meanwhile, the communities in the impacted catchment did not undergo significant changes between 2012 and 2021, likely influenced by the effects of prolonged droughts following floods after 2018. The results of our study confirm the significance of restoration and land-use management in fostering long-term improvements in stream communities, while climate change remains a prodigious threat. The coupling of long-term biodiversity monitoring with concurrent sampling of relevant environmental drivers is critical for preventative and restorative management in ecology.


Wirbel, J., Bhatt, A.S., Probst, A.J. (2024) The journey to understand previously unknown microbial genes. Nature, 626(7998), 267-269. https://doi.org/10.1038/d41586-024-00077-w

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The topic in brief

• Some aspects of microbiology remain mysterious because of a lack of information about the identity and role of many microbial genes and proteins.

• The ability to obtain and analyse microbial sequences at scale and across species, including those that cannot be grown under laboratory conditions, are providing insights and data to explore.

Writing in Nature, Rodríguez del Río et al.1 report their analysis of 149,842 bacterial genomes sampled from a variety of habitats in the wild.

• The data were used to select sequences to generate a catalogue of 404,085 previously unknown gene families that could be prioritized for further study.

• The investigation of these previously unknown genes could lead to new clinical tools or offer fresh perspectives about how microorganisms evolved to survive in their natural environments.


Gillmann, S.M., Lorenz, A.W., Kaijser, W., Nguyen, H.H., Haase, P., Hering, D. (2024) How tolerances, competition and dispersal shape benthic invertebrate colonisation in restored urban streams. Science of the Total Environment, 929, 172665. https://doi.org/10.1016/j.scitotenv.2024.172665

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Abstract

Biotic communities often respond poorly to river restoration activities and the drivers of community recovery after restoration are not fully understood. According to the Asymmetric Response Concept (ARC), dispersal capacity, species tolerances to stressors, and biotic interactions are three key drivers influencing community recovery of restored streams. However, the ARC remains to be tested. Here we used a dataset on benthic invertebrate communities of eleven restored stream sections in a former open sewer system that were sampled yearly over a period of eleven years. We applied four indices that reflect tolerance against chloride and organic pollution, the community's dispersal capacity and strength of competition to the benthic invertebrate taxa lists of each year and site. Subsequently, we used generalised linear mixed models to analyse the change of these indices over time since restoration. Dispersal capacity was high directly after restoration but continuously decreased over time. The initial communities thus consisted of good dispersers and were later joined by more slowly dispersing taxa. The tolerance to organic pollution also decreased over time, reflecting continuous improvement of water quality and an associated increase of sensitive species. On the contrary, chloride tolerances did not change, which could indicate a stable chloride level throughout the sampling period. Lastly, competition within the communities, reflected by interspecific trait niche overlap, increased with time since restoration. We show that recovery follows a specific pattern that is comparable between sites. Benthic communities change from tolerant, fast dispersing generalists to more sensitive, slowly dispersing specialists exposed to stronger competition. Our results lay support to the ARC (increasing role of competition, decreasing role of dispersal) but also underline that certain tolerances may still shape communities a decade after restoration. Disentangling the drivers of macroinvertebrate colonisation can help managers to better understand recovery trajectories and to define more realistic restoration targets.


Schlenker, A., Brauns, M., Fink, P., Lorenz, A.W., Weitere, M. (2024) Long-term recovery of benthic food webs after stream restoration. Science of the Total Environment, 923, 171499. https://doi.org/10.1016/j.scitotenv.2024.171499

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The assessment of restoration success often neglects trophic interactions within food webs, focusing instead on biodiversity and community structure. Here, we analysed the long-term recovery of food web structure based on stable isotopes (δ13C and δ15N) of benthic invertebrates and quantified responses of food web metrics to time since restoration. The samples derived from twelve restored sites with different restoration ages, sampled annually from 2012 to 2021, and covering an investigation period of up to 28 years after restoration for the whole catchment. Temporal developments of the restored sites were compared to the development of two near-natural sites. The restoration measures consisted of the cessation of sewage inflow and morphological restoration of the channels. As a clear and consistent result over almost all sites, trophic similarity (proportion of co-existing species occupying similar trophic niches) increased with time since restoration, and reached values of near-natural sites, suggesting an increase in the stability and resilience of the food webs. Surprisingly, resource diversity decreased at most restored sites within 10 years after restoration, probably due to the removal of wastewater-derived resources, and a shift towards leaf litter as the dominant resource following the regrowth of the riparian vegetation. Food chain length showed no consistent pattern over time at the different sites both increasing and decreasing with time since restoration. Overall, restoration had clear effects on the food web structure of stream ecosystems. While some effects such as the increase in trophic similarity were consistent at almost all sites, others such as response of the food chain length were context dependent. The study demonstrates the potential of utilizing food web metrics, particularly trophic similarity, in restoration research to achieve a more holistic understanding of ecosystem recovery.


Bayat, H.S., Enß, J., Escobar-Sierra, C., Gillmann, S.M., Khaliq, S., Kuppels, A., [. . .], Vos, M. (2024) Solving the puzzle of ecosystem recovery. Frontiers for Young Minds, 12, 1302974. https://doi.org/10.3389/frym.2024.1302974

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Human activities, past and present, have a big impact on nature, affecting ecosystems in profound ways. Scientists are working hard to figure out the best methods to restore damaged ecosystems. But ecosystem restoration often does not go as planned, resulting in very different ecosystems than before. For example, some animals that used to live in an ecosystem can take a long time to return or do not come back at all. To understand the complexities of ecosystem recovery, scientists have come up with a theory called the asymmetric response concept (ARC), to understand how ecosystems recover. The ARC helps us describe the various responses that can happen after ecosystem damage and why the responses happen that way. Once we understand these responses, we can help ecosystems become healthy again. By learning how organisms rejoin damaged ecosystems, we can better protect our environment for the future.


Madge Pimentel, I., Baikova, D., Buchner, D., Burfeid Castellanos, A., David, G.M., Deep, A., [. . .], Beermann, A.J. (2024) Assessing the response of an urban stream ecosystem to salinization under different flow regimes. Science of the Total Environment, 926, 171849. https://doi.org/10.1016/j.scitotenv.2024.171849

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Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.


Escobar-Sierra, C., Lampert, K.P. (2024) Field application of de novo transcriptomic analysis to evaluate the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams. PLoS One, 19(3), e0298213. https://doi.org/10.1371/journal.pone.0298213

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Freshwater salinization poses global challenges for aquatic organisms inhabiting urban streams, impacting their physiology and ecology. However, current salinization research predominantly focuses on mortality endpoints in limited model species, overlooking the sublethal effects on a broader spectrum of organisms and the exploration of adaptive mechanisms and pathways under natural field conditions. To address these gaps, we conducted high-throughput sequencing transcriptomic analysis on the gill tissue of the euryhaline fish Gasterosteus aculeatus, investigating its molecular response to salinity stress in the highly urbanized river Boye, Germany. We found that in stream sections with sublethal concentrations of chloride costly osmoregulatory systems were activated, evidenced by the differential expression of genes related to osmoregulation. Our enrichment analysis revealed differentially expressed genes (DEGs) related to transmembrane transport and regulation of transport and other osmoregulation pathways, which aligns with the crucial role of these pathways in maintaining biological homeostasis. Notably, we identified candidate genes involved in increased osmoregulatory activity under salinity stress, including those responsible for moving ions across membranes: ion channels, ion pumps, and ion transporters. Particularly, genes from the solute carrier family SLC, aquaporin AQP1, chloride channel CLC7, ATP-binding cassette transporter ABCE1, and ATPases member ATAD2 exhibited prominent differential expression. These findings provide insights into the potential molecular mechanisms underlying the adaptive response of euryhaline fish to salinity stress and have implications for their conservation and management in the face of freshwater salinization.


Markert, N., Schürings, C., Feld, C.K. (2024) Water Framework Directive micropollutant monitoring mirrors catchment land use: Importance of agricultural and urban sources revealed. Science of the Total Environment, 917, 170583. https://doi.org/10.1016/j.scitotenv.2024.170583

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Research gate
Abstract

River monitoring programs worldwide consistently unveil micropollutant concentrations (pesticide, pharmaceuticals, and industrial chemicals) exceeding regulatory quality targets with deteriorating effects on aquatic communities. However, both the composition and individual concentrations of micropollutants are likely to vary with the catchment land use, in particular regarding urban and agricultural area as the primary sources of micropollutants. In this study, we used a dataset of 109 governmental monitoring sites with micropollutants monitored across the Federal State of North Rhine-Westphalia, Germany, to investigate the relationship between high-resolution catchment land use (distinguishing urban, forested and grassland area as well as 22 different agricultural crop types) and 39 micropollutants using Linear Mixed Models (LMMs). Ecotoxicological risks were indicated for mixtures of pharmaceutical and industrial chemicals for 100 % and for pesticides for 55 % of the sites. The proportion of urban area in the catchment was positively related with concentrations of most pharmaceuticals and industrial chemicals (R2 up to 0.54), whereas the proportions of grassland and forested areas generally showed negative relations. Cropland overall showed weak positive relationships with micropollutant concentrations (R2 up to 0.29). Individual crop types, particularly vegetables and permanent crops, showed higher relations (R2 up to 0.46). The findings suggest that crop type-specific pesticide applications are mirrored in the detected micropollutant concentrations. This highlights the need for high-resolution spatial land use to investigate the magnitude and dynamics of micropollutant exposure and relevant pollution sources, which would remain undetected with highly aggregated land use classifications. Moreover, the findings imply the need for tailored management measures to reduce micropollutant concentrations from different sources and their related ecological effects. Urban point sources, could be managed by advanced wastewater treatment. The reduction of diffuse pollution from agricultural land uses requires additional measures, to prevent pesticides from entering the environment and exceeding regulatory quality targets.


Mack, L., Buchner, D., Brasseur, M.V., Kaijser, W., Leese, F., Piggott, J.J., [. . .], Hering, D. (2024) Fine sediment and the insecticide chlorantraniliprole inhibit organic‐matter decomposition in streams through different pathways. Freshwater Biology, 69, 365–375. https://doi.org/10.1111/fwb.14216

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  1. Intensive agriculture drives an ongoing deterioration of stream biodiversity and ecosystem functioning across the planet. Key agricultural stressors include increased deposited fine sediment and insecticides flushed from adjacent land into streams. The individual and combined effects on aquatic biota are increasingly studied, but the functional consequences of biodiversity loss associated with agricultural stressors remain poorly understood. We addressed this knowledge gap by examining the effects of fine sediment and different concentrations of the insecticide chlorantraniliprole on organic-matter decomposition.
  2. We conducted an outdoor stream mesocosm experiment. Mesocosms contained a standardised organic-matter assay (the cotton-strip assay), which was used to assess organic-matter decomposition rates (as tensile-strength loss of the fabric) and microbial respiration of the cotton strips.
  3. The decomposition rate of strips buried under fine sediment was inhibited, a result we attribute to the limited accessibility for invertebrate feeding and microbial activities, as well as the limited nutrient and dissolved oxygen exchange. The insecticide also inhibited decay rates, a finding we relate to reduced invertebrate grazing and associated excessive algal growth. In contrast to decomposition rates, we did not observe stressor effects on microbial respiration. An interaction between fine sediment and chlorantraniliprole was not identified.
  4. Our results suggest that stressors induced by agriculture affect functions of stream ecosystems through a variety of pathways and operate by modifying habitats and biotic interactions.
  5. By examining a combination of stressors and responses that have not been addressed before, this study gives important insights into the effects of agricultural practices on streams. Understanding the effects of chlorantraniliprole is especially important since it is likely to become more widely used in future agricultural practice due to the increasing ban on neonicotinoid insecticides. Furthermore, most experimental studies address multiple stressor effects on biota. For a comprehensive understanding of complex stressor effects on ecosystems, ecosystem functions also need to be studied, such as the organic-matter decomposition within streams.

Tielke, A.K., Vos, M. (2024) Successful reintroduction of species: improving on windows of opportunity for biodiversity repair. Restoration Ecology, 32(3), e14091. https://doi.org/10.1111/rec.14091

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Research gate
Abstract

To overcome resistance of degraded ecological communities to restorative interventions, we need to understand windows of opportunity—limited time frames when species reintroduction attempts are still successful. More specifically, we need to understand what makes these windows close, as this may enable us to stretch or reopen them. We investigated this using models of simple food web modules. We show how joint changes of bottom–up and top–down control may be applied to change windows of opportunity and increase reintroduction success. Which reintroduction densities were most effective seemed system-specific. A more general result is that reintroduction success was strongly enhanced by low to intermediate carrying capacities of basal species (e.g. periphyton and other algae in streams). This can be seen as equivalent to low to intermediate nutrient levels. When these were too high, almost any combination of restorative measures was rendered ineffective. Interestingly, reintroducing primarily and secondarily lost species at the same time was more effective than sequential reintroductions that first attempted to fix secondary extinctions. We could further enhance the success of species reintroductions by reducing the carrying capacities of basal species before the reintroduction of primarily and secondarily lost species. We discuss our results in the light of empirical work on macro-invertebrates in streams. This serves to exemplify how our results can be applied in the practice of ecological restoration.


Schürings, C., Hering, D., Kaijser, W., Kail, J. (2024) Assessment of cultivation intensity can improve the correlative strength between agriculture and the ecological status in rivers across Germany. Agriculture, Ecosystems & Environment, 361, 108818. https://doi.org/10.1016/j.agee.2023.108818

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Research gate
Abstract

Agriculture has been identified as a main cause for more than 90% of Germany´s rivers still not meeting good ecological status in 2021. While many large-scale studies observed a negative effect of catchment agricultural land use on river biota, they rarely considered differences in cultivation intensities, although small-scale studies highlight clear differences between the effects of agricultural crops. Here we used Germany-wide and spatially explicit information on crop types to calculate agricultural intensity indices for nutrients and pesticides, weighting different crop types based on average pesticide treatment and nutrient application rates. These indices were then used as explanatory variables for the ecological status of n = 7677 biological sampling sites. Pesticides were more important than nutrient pollution for macroinvertebrates and macrophytes, while diatoms were more sensitive to nutrients. Considering the most relevant intensity index (pesticide or nutrient) slightly increased the correlative strength with ecological status, as compared to the correlation with agricultural land or cropland cover by up to R2 = 0.14 for diatoms. Correlative strength of agricultural intensity indices was substantially larger in small mountain and (pre)-alpine streams compared to lowland streams, with an R2 up to 0.43 for macroinvertebrates. These results not only confirm previous large-scale studies by demonstrating the detrimental effects of present-day agriculture on river biota, but also shed light on the main pathways involved, particularly highlighting the adverse impacts of agrochemicals. Consequently, to protect river biota, a shift to more sustainable agricultural practices, like reducing pesticide application, is urgently required.


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2024

Simon, S.A., Aschmann, V., Behrendt, A., Hügler, M., Engl, L.M., Pohlner, M., [. . .], Probst, A.J. (2024) Earth's most needed uncultivated aquatic prokaryotes. Water Research. https://doi.org/10.1016/j.watres.2024.122928

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Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.

Khaliq, S., Jochmann, M.A., Hesse, T., Nachev, M., Sures, B., Riekenberg, P.M., [. . .], Schmidt, T.C. (2024) Compound-specific isotope analysis of amino acids for aquatic systems – Problems, challenges, solutions: A review. TrAC Trends in Analytical Chemistry, 181. https://doi.org/10.1016/j.trac.2024.118038

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Compound-specific isotope analysis of individual amino acids (AAs) is a promising method for characterizing resource flow and transformation in aquatic systems, encompassing microbial domains to macroscopic consumers. This review delves into two key areas of research concerning AAs in aquatic ecosystems. Firstly, carbon isotope analysis is employed to explore carbon sources assimilated for AAs synthesis, and secondly, nitrogen isotope analysis is used to clarify ecosystem baselines and trophic dynamics of organisms. Surprisingly, literature provides limited discussions on the limitations or critical challenges faced during AAs isotope analysis over the past decade. To address this gap, this review focuses on challenges encountered in method development, sample preparation, and technical aspects, including instrumental design, and δ13C and δ15N analysis of AAs. Recommendations are provided to increase the accuracy and reliability. The review also highlights the significance of comprehensive understanding and detailed methodology to address challenges during AA isotope analysis in aquatic systems.

Venkataramanan, A., Kloster, M., Burfeid-Castellanos, A., Dani, M., Mayombo, N.A.S., Vidakovic, D., [. . .], Beszteri, B. (2024) "UDE DIATOMS in the Wild 2024": a new image dataset of freshwater diatoms for training deep learning models. Gigascience, 13. https://doi.org/10.1093/gigascience/giae087

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Background

Diatoms are microalgae with finely ornamented microscopic silica shells. Their taxonomic identification by light microscopy is routinely used as part of community ecological research as well as ecological status assessment of aquatic ecosystems, and a need for digitalization of these methods has long been recognized. Alongside their high taxonomic and morphological diversity, several other factors make diatoms highly challenging for deep learning–based identification using light microscopy images. These include (i) an unusually high intraclass variability combined with small between-class differences, (ii) a rather different visual appearance of specimens depending on their orientation on the microscope slide, and (iii) the limited availability of diatom experts for accurate taxonomic annotation.

Findings

We present the largest diatom image dataset thus far, aimed at facilitating the application and benchmarking of innovative deep learning methods to the diatom identification problem on realistic research data, “UDE DIATOMS in the Wild 2024.” The dataset contains 83,570 images of 611 diatom taxa, 101 of which are represented by at least 100 examples and 144 by at least 50 examples each. We showcase this dataset in 2 innovative analyses that address individual aspects of the above challenges using subclustering to deal with visually heterogeneous classes, out-of-distribution sample detection, and semi-supervised learning.

Conclusions

The problem of image-based identification of diatoms is both important for environmental research and challenging from the machine learning perspective. By making available the so far largest image dataset, accompanied by innovative analyses, this contribution will facilitate addressing these points by the scientific community.


Farias, L., Beszteri, B., Burfeid Castellanos, A., Doliwa, A., Enss, J., Feld, C.K., [. . .], Le, T.T.Y. (2024) Influence of salinity on the thermal tolerance of aquatic organisms. Science of the Total Environment, 953, 176120. https://doi.org/10.1016/j.scitotenv.2024.176120

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Aquatic organisms are challenged by changes in their external environment, such as temperature and salinity fluctuations. If these variables interacted with each other, the response of organisms to temperature changes would be modified by salinity and vice versa. We tested for potential interaction between temperature and salinity effects on freshwater, brackish, and marine organisms, including algae, macrophytes, heterotrophic protists, parasites, invertebrates, and fish. We performed a meta-analysis that compared the thermal tolerance (characterised by the temperature optimum, lower and upper temperature limits, and thermal breadth) at various salinities. The meta-analysis was based on 90 articles (algae: 15; heterotrophic protists: 1; invertebrates: 43; and fish: 31). Studies on macrophytes and parasites were lacking. We found that decreasing salinity significantly increased and decreased the lower and upper temperature limits, respectively, in all groups. Thus, a lowered salinity increased the thermal sensitivity of organisms. These findings mainly reflect the response of brackish and marine organisms to salinity changes, which dominated our database. The few studies on freshwater species showed that their lower thermal limits increased and the upper thermal limits decreased with increasing salinity, albeit statistically nonsignificant. Although non-significant, the response of thermal tolerance to salinity changes differed between various organism groups. It generally decreased in the order of: algae > invertebrates > fish. Overall, our findings indicate adverse effects of salinity changes on the temperature tolerance of aquatic organisms. For freshwater species, studies are comparatively scarce and further studies on their thermal performance at various salinity gradients are required to obtain more robust evidence for interactions between salinity and temperature tolerance. Considering test conditions such as acclimation temperature and potential infection with parasites in future studies may decrease the variability in the relationship between salinity and thermal tolerance.


Mayombo, N.A.S., Dani, M., Kloster, M., Vidaković, D., Buchner, D., Burfeid-Castellanos, A.M., Beszteri, B. (2024) Assessment of microphytobenthos communities in the Kinzig catchment using photosynthesis-related traits, digital light microscopy and 18S-V9 amplicon sequencing. Frontiers in Ecology and Evolution, 12. https://doi.org/10.3389/fevo.2024.1422925

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Introduction: Microalgae form an essential group of benthic organisms that respond swiftly to environmental changes. They are widely used as bioindicators of anthropogenic stressors in freshwater ecosystems. We aimed to assess the responses of microalgae communities to multiple environmental stressors in the Kinzig River catchment, home to a long-term ecological monitoring site, in Germany.

Methods: We used a photosynthetic biomass proxy alongside community composition of diatoms assessed by digital light microscopy, and of microalgae by 18S-V9 amplicon sequencing, to characterise microalgae at 19 sampling sites scattered across the catchment.

Results: Our results revealed significant effects of physical and chemical factors on microalgae biomass and community compositions. We found that conductivity, water temperature and pH were the most important factors affecting microalgae community composition, as observed in both microscopy and amplicon analysis. In addition to these three variables, the effect of total phosphate on all microalgae, together with water discharge on the diatom (Bacillariophyta) communities, as assessed by amplicon analysis, may reveal taxon-specific variations in the ecological responses of different microalgal groups.

Discussion: Our results highlighted the complex relationship between various environmental variables and microalgae biomass and community composition. Further investigations, involving the collection of time series data, are required to fully understand the underlying biotic and abiotic parameters that influence these microalgae communities.


Boden, L., Klagus. C., Boenigk, J. (2024) Insights from single-strain and mixed culture experiments on the effects of heatwaves on freshwater flagellates. PeerJ, 12:e17912. http://doi.org/10.7717/peerj.17912

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The increasing frequency and intensity of heatwaves driven by climate change significantly impact microbial communities in freshwater habitats, particularly eukaryotic microorganisms. Heterotrophic nanoflagellates are important bacterivorous grazers and play a crucial role in aquatic food webs, influencing the morphological and taxonomic structure of bacterial communities. This study investigates the responses of three flagellate taxa to heatwave conditions through single-strain and mixed culture experiments, highlighting the impact of both biotic and abiotic factors on functional redundancy between morphologically similar protist species under thermal stress. Our results indicate that temperature can significantly impact growth and community composition. However, density-dependent factors also had a significant impact. In sum, stabilizing effects due to functional redundancy may be pronounced as long as density-dependent factors play a minor role and can be overshadowed when flagellate abundances increase.


Kuppels, A., Bayat, H.S., Gillmann, S.M., Schäfer, R.B., Vos, M. (2024) Putting the Asymmetric Response Concept to the test: modelling multiple stressor exposure and release in a stream food web. Science of the Total Environment, 174722. https://doi.org/10.1016/j.scitotenv.2024.174722

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Communities in stream ecosystems often respond asymmetrically to increase and release of stressors, as indicated by slow and incomplete recovery. The Asymmetric Response Concept (ARC) posits that this is due to a shift in the relative importance of three mechanisms: tolerance, dispersal, and biotic interactions. In complex natural communities, these mechanisms may produce alternative outcomes through poorly understood indirect effects. To understand how the three mechanisms respond to different temporal stressor scenarios, we studied multiple scenarios using a stream food web model. We asked the following questions: Do groups of species decline as expected on the basis of individual tolerance rankings derived from laboratory experiments when they are embedded in a complex dynamic food web?

Does the response of ecosystem function match that of communities? To address these questions, we aggregated data on individual tolerances at the level of functional groups and studied how single and multiple stressors affect food web dynamics and nutrient cycling. Multiple stressor scenarios involved different intensities of salt and temperature increase. Functional groups exhibited a different relative tolerance ranking between the laboratory and dynamic food web contexts. Salt as a single stressor had only minor and transient effects at low level but led to the loss of one or more functional groups at high level. In contrast, high temperature, alone or in combination with salt, caused the loss of functional groups at all tested levels. Patterns often differed between the response of communities and ecosystem function. We discuss our findings with respect to the ARC.


Mayombo, N.A.S., Burfeid-Castellanos, A.M., Vermiert, A.M., Pimentel, I.M., Rehsen, P.M., Dani, M., [. . .], Beszteri, B. (2024) Functional and compositional responses of stream microphytobenthic communities to multiple stressors increase and release in a mesocosm experiment. Science of the Total Environment, 943, 173670. https://doi.org/10.1016/j.scitotenv.2024.173670

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Field observations form the basis of the majority of studies on microphytobenthic algal communities in freshwater ecosystems. Controlled mesocosm experiments data are comparatively uncommon. The few experimental mesocosm studies that have been conducted provide valuable insights into how multiple stressors affect the community structures and photosynthesis-related traits of benthic microalgae. The recovery process after the stressors have subsided, however, has received less attention in mesocosm studies. To close this gap, here we present the results of a riparian mesocosm experiment designed to investigate the effects of reduced flow velocity, increased salinity and increased temperature on microphytobenthic communities. We used a full factorial design with a semi-randomised distribution of treatments consisting of two levels of each stressor (2 × 2 × 2 treatments), with eight replicates making a total of 64 circular mesocosms, allowing a nuanced examination of their individual and combined influences. We aimed to elucidate the responses of microalgae communities seeded from stream water to the applied environmental stressors. Our results showed significant effects of reduced flow velocity and increased temperature on microphytobenthic communities. Recovery after stressor treatment led to a convergence in community composition, with priority effects (hypothesized to reflect competition for substrate between resident and newly arriving immigrant taxa) slowing down community shifts and biomass increase. Our study contributes to the growing body of literature on the ecological dynamics of microphytobenthos and emphasises the importance of rigorous experiments to validate hypotheses. These results encourage further investigation into the nuanced interactions between microphytobenthos and their environment and shed light on the complexity of ecological responses in benthic systems.


Escobar-Sierra, C., Cañedo-Argüelles, M., Vinyoles, D., Lampert, K.P. (2024) Unraveling the molecular mechanisms of fish physiological response to freshwater salinization: A comparative multi-tissue transcriptomic study in a river polluted by potash mining. Environmental Pollution, 357, 124400. https://doi.org/10.1016/j.envpol.2024.124400

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Freshwater salinization is an escalating global environmental issue that threatens freshwater biodiversity, especially fish populations. This study aims to uncover the molecular basis of salinity physiological responses in a non-native minnow species (Phoxinus septimaniae x P. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge) were examined. Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity physiological response in non-native minnows confronting diverse environmental stressors. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish physiological response in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing salinization.


Markert, N., Guhl, B., Feld, C.K. (2024) Linking wastewater treatment plant effluents to water quality and hydrology: Effects of multiple stressors on fish communities. Water Research, 260, 121914. https://doi.org/10.1016/j.watres.2024.121914

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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.


Enss, J., Nachev, M., Jochmann, M.A., Schmidt, T.C., Feld, C.K. (2024) Stable isotopes (15N) facilitate non‐invasive labelling of large quantities of macroinvertebrates across different species and feeding types. Ecology and Evolution, 14(6), e11539. https://doi.org/10.1002/ece3.11539

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While macroinvertebrate dispersal operates at the individual level, predictions of their dispersal capabilities often rely on indirect proxies rather than direct measurements. To gain insight into the dispersal of individual specimens, it is crucial to mark (label) and capture individuals. Isotopic enrichment with 15N is a non-invasive method with the potential of labelling large quantities of macroinvertebrates. While the analysis of 15N is widely utilised in food web studies, knowledge on the specific utility of isotopic enrichment with 15N for mass labelling of macroinvertebrate individuals across different taxa and feeding types is limited.

Previous studies have focused on single species and feeding types, leaving gaps in our understanding of the broader applicability of this method. Therefore, this study aimed to test and compare isotopic mass enrichment across several macroinvertebrate taxa and feeding types. We released 15NH4Cl at five stream reaches in North-Rhine Westphalia, Germany, and successfully enriched 12 distinct macroinvertebrate taxa (Crustacea and Insecta).

Significant enrichment was achieved in active and passive filter feeders, grazers, shredders and predators, and predominantly showed positive correlations with the enrichment of the taxa's main food sources phytobenthos and particulate organic matter. Enrichment levels rose rapidly and peaked at distances between 50 m and 300 m downstream of the isotopic inlet; significant enrichment occurred up to 2000 m downstream of the isotopic inlet in all feeding types. Macroinvertebrate density estimates on the stream bottom averaged to a total of approximately 3.4 million labelled individuals of the 12 investigated taxa, thus showing the high potential of isotopic (15N) enrichment as a non-invasive method applicable for mass labelling across different macroinvertebrate feeding types. Hence, isotopic enrichment can greatly assist the analysis of macroinvertebrate dispersal through mark-and-recapture experiments, as it allows to measure the movement at the level of individual specimens.


David, G.M., Madge Pimentel, I., Rehsen, P.M., Vermiert, A.M., Leese, F., Gessner, M.O. (2024) Multiple stressors affecting microbial decomposer and litter decomposition in restored urban streams: Assessing effects of salinization, increased temperature, and reduced flow velocity in a field mesocosm experiment. Science of the Total Environment, 934, 173669. https://doi.org/10.1016/j.scitotenv.2024.173669

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A multitude of anthropogenic stressors impact biological communities and ecosystem processes in urban streams. Prominent among them are salinization, increased temperature, and altered flow regimes, all of which can affect microbial decomposer communities and litter decomposition, a fundamental ecosystem process in streams. Impairments caused by these stressors individually or in combination and recovery of communities and ecosystem processes after release from these stressors are not well understood. To improve our understanding of multiple stressors impacts we performed an outdoor stream mesocosm experiment with 64 experimental units to assess the response of microbial litter decomposers and decomposition. The three stressors we applied in a full-factorial design were increased salinity (NaCl addition, 0.53 mS cm-1 above ambient), elevated temperature (3.5 °C above ambient), and reduced flow velocity (3.5 vs 14.2 cm s-1). After two weeks of stressor exposure (first sampling) and two subsequent weeks of recovery (second sampling), we determined leaf-associated microbial respiration, fungal biomass, and the sporulation activity and community composition of aquatic hyphomycetes in addition to decomposition rates of black alder (Alnus glutinosa) leaves confined in fine-mesh litter bags. Microbial colonization of the litter was accompanied by significant mass loss in all mesocosms. However, there was little indication that mass loss, microbial respiration, fungal biomass, sporulation rate or community composition of aquatic hyphomycetes was strongly affected by either single stressors or their interactions. Two exceptions were temperature effects on sporulation and decomposition rate. Similarly, no notable differences among mesocosms were observed after the recovery phase. These results suggest that microbial decomposers and leaf litter decomposition are either barely impaired by exposure to the tested stressors at the levels applied in our experiment, or that communities in restored urban streams are well adapted to cope with these stressor levels.


Peters, K., Grantz, S.F., Kiesel, J., Lewandowski, J., Fohrer, N. (2024) Hyporheic exchange flows in a mountainous river catchment identified by distributed temperature sensing. River Research and Applications. https://doi.org/10.1002/rra.4306

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Elevated stream temperatures under low-flows, exacerbated by global warming, are a stressor that affects aquatic species directly or in combination with other stressors. Stream temperatures are influenced by energy fluxes across the air–water interface as well as by hydrological exchange processes occurring at the water–riverbed interface. Small-scale stream temperature dynamics influenced by exchange flows are still underrepresented in stream temperature research. To investigate high-resolution temperature dynamics and hydrological exchange processes at the sediment–water interface we applied fiber-optic distributed temperature sensing (FO-DTS) at two sites in the mountainous Kinzig catchment combined with mapping and measurement of additional environmental conditions. Two types of temperature anomalies could be observed at one site under conditions of low flow and high air temperature. Dampening effects coincided with riverine features such as pools, vegetation roots, fine sediment, and signs of streambank seepage which indicated hyporheic exchange flows. Increased heating of the substrate during the day was identified in shallow sections where sediment was exposed to the air and shading from riparian vegetation was patchy. At another site, at which the cable could not be buried because of the sediment composition, temperature anomalies in the overlying water indicated diffuse groundwater exfiltration. The results show that small-scale processes in the hyporheic zone, low water tables, and riparian shading influence stream temperature in mountainous streams and can be identified with FO-DTS under suitable conditions. The results improve our understanding of stream temperatures (in the hyporheic zone) and provide important information on how to improve hydrological modeling.


Medina Madariaga, G., Ferreira, V., Arora, R., Mansour, I., David, G.M., Jähnig, S.C., He, F. (2024) Multiple‐stressor effects on leaf litter decomposition in freshwater ecosystems: A meta‐analysis. Functional Ecology, 38(7), 1523-1536. https://doi.org/10.1111/1365-2435.14571

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  1. Recent years have witnessed a surge in research on the effects of multiple stressors in freshwater ecosystems. While studies have increased, the synthesis of their findings into a broader understanding of ecosystem-level effects remains an ongoing endeavour. Leaf litter decomposition, a frequently investigated and pivotal ecosystem function in freshwaters, is sensitive to changes in abiotic conditions and biotic communities, and therefore susceptible to multiple-stressor effects.
  2. Here, we synthesize findings from 27 manipulative experimental studies encompassing 61 responses of litter decomposition to paired stressors such as warming, nutrient enrichment and emerging pollutants in freshwater ecosystems. We calculated the individual and overall interaction effect sizes resulting from two stressors occurring simultaneously. Furthermore, we analysed the effect of moderator variables in the size and direction of interaction effect sizes using a meta-analytical approach.
  3. Although the vote-counting method showed additive interactions to dominate individual observations (91.8%), weighted random-effects meta-analysis revealed an overall antagonistic interaction between stressors (i.e. the cumulative effect of paired stressors on litter decomposition was less than the sum of their single effects). Our results emphasized the influence of experimental characteristics such as macroinvertebrate involvement, habitat type (lentic vs. lotic) and litter quality (assumed from plant mycorrhizal association) in shaping the responses of litter decomposition to multiple stressors.
  4. Our meta-analysis highlights the need to incorporate local ecological complexities in manipulative experiments to improve predictions of multiple-stressor effects on biodiversity and ecosystem functions. The present study underscores the importance of considering biotic interactions and adopting the metacommunity framework in conservation and restoration actions to support the management of freshwater ecosystems in an era of rapid global change.

Kaijser, W., Lorenz, A.W., Brauer, V.S., Burfeid Castellanos, A., David, G.M., Nuy, J.K., [. . .], Hering, D. (2024) Differential associations of five riverine organism groups with multiple stressors. Science of the Total Environment, 934, 173105. https://doi.org/10.1016/j.scitotenv.2024.173105

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The decline of river and stream biodiversity results from multiple simultaneous stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish.

Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models.

Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.


Lee, K.S., Landry, Z., Athar, A., Alcolombri, U., Pramoj Na Ayutthaya, P., Berry, D., [. . .], Meckenstock, R., [. . .], Probst, A.J., [. . .], Stocker, R. (2024) MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. Nature Microbiology, 9, 1152–1156 . https://doi.org/10.1038/s41564-024-01656-3

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Here we present the establishment of an open-access web-based repository for microbiological Raman spectroscopy data. The data collection, called ‘MicrobioRaman’ (https://www.ebi.ac.uk/biostudies/MicrobioRaman/studies), was inspired by the great success and usefulness of research databases such as GenBank and UniProt. This centralized repository, residing within the BioStudies database1 — which is maintained by a public institution, the European Bioinformatics Institute — minimizes the risk of data loss or eventual abandonment, offering a long-term common reference for analysis with advantages in accessibility and transparency over commercial data analysis tools. We feel that MicrobioRaman will provide a foundation for this growing field by serving as an open-access repository for sharing microbiological Raman data and through the codification of a set of reporting standards.


Prati, S., Grabner, D.S., Hupało, K., Weiperth, A., Maciaszek, R., Lipták, B., [. . .], Sures, B. (2024) Invisible invaders: range expansion of feral Neocaridina davidi offers new opportunities for generalist intracellular parasites. Biological Invasions. https://doi.org/10.1007/s10530-024-03324-3

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The release of ornamental pets and associated pathogens outside their native range might directly or indirectly impact the recipient community. In temperate regions, e.g., central Europe, feral freshwater species of tropical and sub-tropical origins are mainly constrained to thermally polluted waters and thermal springs. However, species with high environmental plasticity and reproduction rates, such as the shrimp Neocaridina davidi, may adapt to colder water regimes over time. A widening thermal niche may eventually overcome thermal barriers, further expanding the range and enhancing transmission opportunities for host generalist parasites. This study assesses the observed (field observations) and theoretical (species distribution models) range expansion of N. davidi and associated parasites in Europe. We report three newly established N. davidi populations from thermally polluted waters in central Europe (Germany, Hungary, and Slovakia) and provide further evidence of its range expansion into colder environments. Species distribution models predict thermally suitable habitats in the Mediterranean and a foreseeable expansion into Western Europe and the Balkans by 2050. We confirm the presence of the microsporidian parasite Ecytonucleospora hepatopenaei in feral N. davidi populations across Europe and expand the list of microsporidians found in this host from two to four. Furthermore, we provide the first evidence of parasite spillover from/to the invasive crayfish Procambarus clarkii, suggesting that parasite exchange with native biota might be possible. Such possibility, coupled with an ongoing range expansion of N. davidi bolstered by human-mediated introductions and climate change, will likely exacerbate the impact on native biota.


Nguyen, H.H., Peters, K., Kiesel, J., Welti, E.A.R., Gillmann, S.M., Lorenz, A.W., [. . .], Haase, P. (2024) Stream macroinvertebrate communities in restored and impacted catchments respond differently to climate, land-use, and runoff over a decade. Science of the Total Environment, 929, 172659. https://doi.org/10.1016/j.scitotenv.2024.172659

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Identifying which environmental drivers underlie degradation and improvements of ecological communities is a fundamental goal of ecology. Achieving this goal is a challenge due to diverse trends in both environmental conditions and ecological communities across regions, and it is constrained by the lack of long-term parallel monitoring of environmental and community data needed to study causal relationships. Here, we identify key environmental drivers using a high-resolution environmental - ecological dataset, an ensemble of the Soil and Water Assessment Tool (SWAT+) model, and ecological models to investigate effects of climate, land-use, and runoff on the decadal trend (2012−2021) of stream macroinvertebrate communities in a restored urban catchment and an impacted catchment with mixed land-uses in Germany. The decadal trends showed decreased precipitation, increased temperature, and reduced anthropogenic land-uses, which led to opposing runoff trends – with decreased runoff in the restored catchment and increased runoff in the impacted catchment. The two catchments also varied in decadal trends of taxonomic and trait composition and metrics. The most significant improvements over time were recorded in communities of the restored catchment sites, which have become wastewater free since 2007 to 2009. Within the restored catchment sites, community metric trends were primarily explained by land-use and evaporation trends, while community composition trends were mostly associated with precipitation and runoff trends. Meanwhile, the communities in the impacted catchment did not undergo significant changes between 2012 and 2021, likely influenced by the effects of prolonged droughts following floods after 2018. The results of our study confirm the significance of restoration and land-use management in fostering long-term improvements in stream communities, while climate change remains a prodigious threat. The coupling of long-term biodiversity monitoring with concurrent sampling of relevant environmental drivers is critical for preventative and restorative management in ecology.


Wirbel, J., Bhatt, A.S., Probst, A.J. (2024) The journey to understand previously unknown microbial genes. Nature, 626(7998), 267-269. https://doi.org/10.1038/d41586-024-00077-w

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The topic in brief

• Some aspects of microbiology remain mysterious because of a lack of information about the identity and role of many microbial genes and proteins.

• The ability to obtain and analyse microbial sequences at scale and across species, including those that cannot be grown under laboratory conditions, are providing insights and data to explore.

Writing in Nature, Rodríguez del Río et al.1 report their analysis of 149,842 bacterial genomes sampled from a variety of habitats in the wild.

• The data were used to select sequences to generate a catalogue of 404,085 previously unknown gene families that could be prioritized for further study.

• The investigation of these previously unknown genes could lead to new clinical tools or offer fresh perspectives about how microorganisms evolved to survive in their natural environments.


Gillmann, S.M., Lorenz, A.W., Kaijser, W., Nguyen, H.H., Haase, P., Hering, D. (2024) How tolerances, competition and dispersal shape benthic invertebrate colonisation in restored urban streams. Science of the Total Environment, 929, 172665. https://doi.org/10.1016/j.scitotenv.2024.172665

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Biotic communities often respond poorly to river restoration activities and the drivers of community recovery after restoration are not fully understood. According to the Asymmetric Response Concept (ARC), dispersal capacity, species tolerances to stressors, and biotic interactions are three key drivers influencing community recovery of restored streams. However, the ARC remains to be tested. Here we used a dataset on benthic invertebrate communities of eleven restored stream sections in a former open sewer system that were sampled yearly over a period of eleven years. We applied four indices that reflect tolerance against chloride and organic pollution, the community's dispersal capacity and strength of competition to the benthic invertebrate taxa lists of each year and site. Subsequently, we used generalised linear mixed models to analyse the change of these indices over time since restoration. Dispersal capacity was high directly after restoration but continuously decreased over time. The initial communities thus consisted of good dispersers and were later joined by more slowly dispersing taxa. The tolerance to organic pollution also decreased over time, reflecting continuous improvement of water quality and an associated increase of sensitive species. On the contrary, chloride tolerances did not change, which could indicate a stable chloride level throughout the sampling period. Lastly, competition within the communities, reflected by interspecific trait niche overlap, increased with time since restoration. We show that recovery follows a specific pattern that is comparable between sites. Benthic communities change from tolerant, fast dispersing generalists to more sensitive, slowly dispersing specialists exposed to stronger competition. Our results lay support to the ARC (increasing role of competition, decreasing role of dispersal) but also underline that certain tolerances may still shape communities a decade after restoration. Disentangling the drivers of macroinvertebrate colonisation can help managers to better understand recovery trajectories and to define more realistic restoration targets.


Schlenker, A., Brauns, M., Fink, P., Lorenz, A.W., Weitere, M. (2024) Long-term recovery of benthic food webs after stream restoration. Science of the Total Environment, 923, 171499. https://doi.org/10.1016/j.scitotenv.2024.171499

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The assessment of restoration success often neglects trophic interactions within food webs, focusing instead on biodiversity and community structure. Here, we analysed the long-term recovery of food web structure based on stable isotopes (δ13C and δ15N) of benthic invertebrates and quantified responses of food web metrics to time since restoration. The samples derived from twelve restored sites with different restoration ages, sampled annually from 2012 to 2021, and covering an investigation period of up to 28 years after restoration for the whole catchment. Temporal developments of the restored sites were compared to the development of two near-natural sites. The restoration measures consisted of the cessation of sewage inflow and morphological restoration of the channels. As a clear and consistent result over almost all sites, trophic similarity (proportion of co-existing species occupying similar trophic niches) increased with time since restoration, and reached values of near-natural sites, suggesting an increase in the stability and resilience of the food webs. Surprisingly, resource diversity decreased at most restored sites within 10 years after restoration, probably due to the removal of wastewater-derived resources, and a shift towards leaf litter as the dominant resource following the regrowth of the riparian vegetation. Food chain length showed no consistent pattern over time at the different sites both increasing and decreasing with time since restoration. Overall, restoration had clear effects on the food web structure of stream ecosystems. While some effects such as the increase in trophic similarity were consistent at almost all sites, others such as response of the food chain length were context dependent. The study demonstrates the potential of utilizing food web metrics, particularly trophic similarity, in restoration research to achieve a more holistic understanding of ecosystem recovery.


Bayat, H.S., Enß, J., Escobar-Sierra, C., Gillmann, S.M., Khaliq, S., Kuppels, A., [. . .], Vos, M. (2024) Solving the puzzle of ecosystem recovery. Frontiers for Young Minds, 12, 1302974. https://doi.org/10.3389/frym.2024.1302974

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Human activities, past and present, have a big impact on nature, affecting ecosystems in profound ways. Scientists are working hard to figure out the best methods to restore damaged ecosystems. But ecosystem restoration often does not go as planned, resulting in very different ecosystems than before. For example, some animals that used to live in an ecosystem can take a long time to return or do not come back at all. To understand the complexities of ecosystem recovery, scientists have come up with a theory called the asymmetric response concept (ARC), to understand how ecosystems recover. The ARC helps us describe the various responses that can happen after ecosystem damage and why the responses happen that way. Once we understand these responses, we can help ecosystems become healthy again. By learning how organisms rejoin damaged ecosystems, we can better protect our environment for the future.


Madge Pimentel, I., Baikova, D., Buchner, D., Burfeid Castellanos, A., David, G.M., Deep, A., [. . .], Beermann, A.J. (2024) Assessing the response of an urban stream ecosystem to salinization under different flow regimes. Science of the Total Environment, 926, 171849. https://doi.org/10.1016/j.scitotenv.2024.171849

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Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.


Escobar-Sierra, C., Lampert, K.P. (2024) Field application of de novo transcriptomic analysis to evaluate the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams. PLoS One, 19(3), e0298213. https://doi.org/10.1371/journal.pone.0298213

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Freshwater salinization poses global challenges for aquatic organisms inhabiting urban streams, impacting their physiology and ecology. However, current salinization research predominantly focuses on mortality endpoints in limited model species, overlooking the sublethal effects on a broader spectrum of organisms and the exploration of adaptive mechanisms and pathways under natural field conditions. To address these gaps, we conducted high-throughput sequencing transcriptomic analysis on the gill tissue of the euryhaline fish Gasterosteus aculeatus, investigating its molecular response to salinity stress in the highly urbanized river Boye, Germany. We found that in stream sections with sublethal concentrations of chloride costly osmoregulatory systems were activated, evidenced by the differential expression of genes related to osmoregulation. Our enrichment analysis revealed differentially expressed genes (DEGs) related to transmembrane transport and regulation of transport and other osmoregulation pathways, which aligns with the crucial role of these pathways in maintaining biological homeostasis. Notably, we identified candidate genes involved in increased osmoregulatory activity under salinity stress, including those responsible for moving ions across membranes: ion channels, ion pumps, and ion transporters. Particularly, genes from the solute carrier family SLC, aquaporin AQP1, chloride channel CLC7, ATP-binding cassette transporter ABCE1, and ATPases member ATAD2 exhibited prominent differential expression. These findings provide insights into the potential molecular mechanisms underlying the adaptive response of euryhaline fish to salinity stress and have implications for their conservation and management in the face of freshwater salinization.


Markert, N., Schürings, C., Feld, C.K. (2024) Water Framework Directive micropollutant monitoring mirrors catchment land use: Importance of agricultural and urban sources revealed. Science of the Total Environment, 917, 170583. https://doi.org/10.1016/j.scitotenv.2024.170583

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Research gate
Abstract

River monitoring programs worldwide consistently unveil micropollutant concentrations (pesticide, pharmaceuticals, and industrial chemicals) exceeding regulatory quality targets with deteriorating effects on aquatic communities. However, both the composition and individual concentrations of micropollutants are likely to vary with the catchment land use, in particular regarding urban and agricultural area as the primary sources of micropollutants. In this study, we used a dataset of 109 governmental monitoring sites with micropollutants monitored across the Federal State of North Rhine-Westphalia, Germany, to investigate the relationship between high-resolution catchment land use (distinguishing urban, forested and grassland area as well as 22 different agricultural crop types) and 39 micropollutants using Linear Mixed Models (LMMs). Ecotoxicological risks were indicated for mixtures of pharmaceutical and industrial chemicals for 100 % and for pesticides for 55 % of the sites. The proportion of urban area in the catchment was positively related with concentrations of most pharmaceuticals and industrial chemicals (R2 up to 0.54), whereas the proportions of grassland and forested areas generally showed negative relations. Cropland overall showed weak positive relationships with micropollutant concentrations (R2 up to 0.29). Individual crop types, particularly vegetables and permanent crops, showed higher relations (R2 up to 0.46). The findings suggest that crop type-specific pesticide applications are mirrored in the detected micropollutant concentrations. This highlights the need for high-resolution spatial land use to investigate the magnitude and dynamics of micropollutant exposure and relevant pollution sources, which would remain undetected with highly aggregated land use classifications. Moreover, the findings imply the need for tailored management measures to reduce micropollutant concentrations from different sources and their related ecological effects. Urban point sources, could be managed by advanced wastewater treatment. The reduction of diffuse pollution from agricultural land uses requires additional measures, to prevent pesticides from entering the environment and exceeding regulatory quality targets.


Mack, L., Buchner, D., Brasseur, M.V., Kaijser, W., Leese, F., Piggott, J.J., [. . .], Hering, D. (2024) Fine sediment and the insecticide chlorantraniliprole inhibit organic‐matter decomposition in streams through different pathways. Freshwater Biology, 69, 365–375. https://doi.org/10.1111/fwb.14216

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  1. Intensive agriculture drives an ongoing deterioration of stream biodiversity and ecosystem functioning across the planet. Key agricultural stressors include increased deposited fine sediment and insecticides flushed from adjacent land into streams. The individual and combined effects on aquatic biota are increasingly studied, but the functional consequences of biodiversity loss associated with agricultural stressors remain poorly understood. We addressed this knowledge gap by examining the effects of fine sediment and different concentrations of the insecticide chlorantraniliprole on organic-matter decomposition.
  2. We conducted an outdoor stream mesocosm experiment. Mesocosms contained a standardised organic-matter assay (the cotton-strip assay), which was used to assess organic-matter decomposition rates (as tensile-strength loss of the fabric) and microbial respiration of the cotton strips.
  3. The decomposition rate of strips buried under fine sediment was inhibited, a result we attribute to the limited accessibility for invertebrate feeding and microbial activities, as well as the limited nutrient and dissolved oxygen exchange. The insecticide also inhibited decay rates, a finding we relate to reduced invertebrate grazing and associated excessive algal growth. In contrast to decomposition rates, we did not observe stressor effects on microbial respiration. An interaction between fine sediment and chlorantraniliprole was not identified.
  4. Our results suggest that stressors induced by agriculture affect functions of stream ecosystems through a variety of pathways and operate by modifying habitats and biotic interactions.
  5. By examining a combination of stressors and responses that have not been addressed before, this study gives important insights into the effects of agricultural practices on streams. Understanding the effects of chlorantraniliprole is especially important since it is likely to become more widely used in future agricultural practice due to the increasing ban on neonicotinoid insecticides. Furthermore, most experimental studies address multiple stressor effects on biota. For a comprehensive understanding of complex stressor effects on ecosystems, ecosystem functions also need to be studied, such as the organic-matter decomposition within streams.

Tielke, A.K., Vos, M. (2024) Successful reintroduction of species: improving on windows of opportunity for biodiversity repair. Restoration Ecology, 32(3), e14091. https://doi.org/10.1111/rec.14091

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Research gate
Abstract

To overcome resistance of degraded ecological communities to restorative interventions, we need to understand windows of opportunity—limited time frames when species reintroduction attempts are still successful. More specifically, we need to understand what makes these windows close, as this may enable us to stretch or reopen them. We investigated this using models of simple food web modules. We show how joint changes of bottom–up and top–down control may be applied to change windows of opportunity and increase reintroduction success. Which reintroduction densities were most effective seemed system-specific. A more general result is that reintroduction success was strongly enhanced by low to intermediate carrying capacities of basal species (e.g. periphyton and other algae in streams). This can be seen as equivalent to low to intermediate nutrient levels. When these were too high, almost any combination of restorative measures was rendered ineffective. Interestingly, reintroducing primarily and secondarily lost species at the same time was more effective than sequential reintroductions that first attempted to fix secondary extinctions. We could further enhance the success of species reintroductions by reducing the carrying capacities of basal species before the reintroduction of primarily and secondarily lost species. We discuss our results in the light of empirical work on macro-invertebrates in streams. This serves to exemplify how our results can be applied in the practice of ecological restoration.


Schürings, C., Hering, D., Kaijser, W., Kail, J. (2024) Assessment of cultivation intensity can improve the correlative strength between agriculture and the ecological status in rivers across Germany. Agriculture, Ecosystems & Environment, 361, 108818. https://doi.org/10.1016/j.agee.2023.108818

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Research gate
Abstract

Agriculture has been identified as a main cause for more than 90% of Germany´s rivers still not meeting good ecological status in 2021. While many large-scale studies observed a negative effect of catchment agricultural land use on river biota, they rarely considered differences in cultivation intensities, although small-scale studies highlight clear differences between the effects of agricultural crops. Here we used Germany-wide and spatially explicit information on crop types to calculate agricultural intensity indices for nutrients and pesticides, weighting different crop types based on average pesticide treatment and nutrient application rates. These indices were then used as explanatory variables for the ecological status of n = 7677 biological sampling sites. Pesticides were more important than nutrient pollution for macroinvertebrates and macrophytes, while diatoms were more sensitive to nutrients. Considering the most relevant intensity index (pesticide or nutrient) slightly increased the correlative strength with ecological status, as compared to the correlation with agricultural land or cropland cover by up to R2 = 0.14 for diatoms. Correlative strength of agricultural intensity indices was substantially larger in small mountain and (pre)-alpine streams compared to lowland streams, with an R2 up to 0.43 for macroinvertebrates. These results not only confirm previous large-scale studies by demonstrating the detrimental effects of present-day agriculture on river biota, but also shed light on the main pathways involved, particularly highlighting the adverse impacts of agrochemicals. Consequently, to protect river biota, a shift to more sustainable agricultural practices, like reducing pesticide application, is urgently required.


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2023

Nguyen, H.H., Venohr, M., Gericke, A., Sundermann, A., Welti, E.A.R., Haase, P. (2023) Dynamics in impervious urban and non-urban areas and their effects on run-off, nutrient emissions, and macroinvertebrate communities. Landscape and Urban Planning, 231, 104639. https://doi.org/10.1016/j.landurbplan.2022.104639

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Researchgate
Abstract

Urbanization is a key factor driving water quality and biological communities in freshwater systems. While urbanization impacts on water resources were well-studied in urban areas, few studies have examined the growing impacts in non-urban areas. Here we investigate the spatiotemporal trends of urbanization using high-resolution impervious surface data of both urban and non-urban areas across Germany, and evaluate the urbanization impacts on changes of run-off, nutrient emissions, and macroinvertebrate communities. The emission changes were modelled using the MONERIS-PCRaster tool, while the macroinvertebrate community responses to urbanization were determined using Generalized Least Square models. We find that urbanization expanded by 3.2% from 2006 to 2015 nationwide, and primarily occurred in less-populated regions. The non-urban areas contributed 19.3–19.6% of the imperviousness expansion nationwide, which were equivalent to the ‘unaccounted’ increases of 15.5–15.9% of run-off, 10.6–11.0% of total nitrogen, and 12.5–12.9% of total phosphorus when only emissions from urban areas were modelled. Incorporating the emissions from both urban and non-urban areas revealed significant impacts of urbanization on macroinvertebrate community composition changes, with increases in more pollution-resistant and non-native species (particularly in large rivers), and reductions of more sensitive taxa. The community responses were jointly determined by local catchment characteristics and urbanization stressors. Our results suggest neglected effects of non-urban impervious surfaces and the importance of using impervious surface data instead of urban land classes to better represent urbanization processes and impacts in long-term planning and management of freshwater systems.


Nguyen, H.H., Kiesel, J., Peters, K., Hering, D., Sinclair, J.S., Haase, P. (2023) Stream macroinvertebrate community metrics consistently respond to a spatiotemporal disturbance gradient but composition is more context-dependent. Landscape Ecology, 38, 3133–3151. https://doi.org/10.1007/s10980-023-01769-w

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Abstract

Context

Improving our understanding of how riverine communities respond to anthropogenic change requires spatial comparisons across multiple sites, high-resolution temporal analyses, and examination of both taxa and trait responses. However, studies that encompass all these aspects remain scarce.

Objectives

We used 10 years of annual monitoring data from 14 sampling sites in the Rhine-Main-Observatory (a Long-Term Ecological Research—LTER—site in Germany) to investigate spatiotemporal responses of stream macroinvertebrate communities along anthropogenic disturbance gradients (measured as ‘ecological quality’).

Methods

We examined spatiotemporal changes in various community components, including taxa, traits, metrics summarizing community responses (e.g., richness), and community composition.

Results

Spatially, consistent patterns over a decade of sampling revealed that less-disturbed communities were characterized by higher taxonomic and trait diversity and occurrence of pollution-sensitive taxa. Anthropogenic disturbance tended to become less severe through time, particularly in more upstream sites, likely driven by improvements in land-use and water quality. Conversely, more downstream sites exhibited a lesser degree of improvement (or none at all) likely owing to persistent or cumulative stressors. Overall, taxonomic/trait metrics consistently reflected the magnitude of the environmental improvement, while community composition did not, suggesting a weaker link between community changes and anthropogenic impacts severity.

Conclusion

Our results emphasize the importance of accounting for the variability in community responses to anthropogenic changes, and identifying optimal monitoring strategies to track such responses. In heterogeneous catchments, choosing which community component to focus and where to locate monitoring sites (e.g., monitoring ecological quality for the EU Water Framework Directive) can determine a timely detection of anthropogenic impacts.


Brasseur, M.V., Buchner, D., Mack, L., Schreiner, V.C., Schäfer, R.B., Leese, F., Mayer, C. (2023) Multiple stressor effects of insecticide exposure and increased fine sediment deposition on the gene expression profiles of two freshwater invertebrate species. Environmental Sciences Europe, 35, 81. https://doi.org/10.1186/s12302-023-00785-6

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Abstract

Background

Freshwater ecosystem degradation and biodiversity decline are strongly associated with intensive agricultural practices. Simultaneously occurring agricultural stressors can interact in complex ways, preventing an accurate prediction of their combined effects on aquatic biota. Here, we address the limited mechanistic understanding of multiple stressor effects of two globally important stressors, an insecticide (chlorantraniliprole), and increased fine sediment load and assessed their impact on the transcriptomic profile of two stream macroinvertebrates: the amphipod Gammarus pulex and the caddisfly Lepidostoma basale.

Results

We identified mainly antagonistic stressor interactions at the transcriptional level, presumably because the insecticide adsorbed to fine sediment particles. L. basale, which is phylogenetically more closely related to the insecticide’s target taxon Lepidoptera, exhibited strong transcriptional changes when the insecticide stressor was applied, whereas no clear response patterns were observed in the amphipod G. pulex. These differences in species vulnerability can presumably be attributed to molecular mechanisms determining the cellular affinity toward a stressor as well as differential exposure patterns resulting from varying ecological requirements between L. basale and G. pulex. Interestingly, the transcriptional response induced by insecticide exposure in L. basale was not associated with a disruption of the calcium homeostasis, which is the described mode of action for chlorantraniliprole. Instead, immune responses and alterations of the developmental program appear to play a more significant role.

Conclusions

Our study shows how transcriptomic data can be used to identify multiple stressor effects and to explore the molecular mechanisms underlying stressor-induced physiological responses. As such, stressor effects assessed at the molecular level can inform about modes of action of chemicals and their interplay with non-chemical stressors. We demonstrated that stressor effects vary between different organismic groups and that insecticide effects are not necessarily covered by their described mode of action, which has important implications for environmental risk assessment of insecticides in non-target organisms.


Kaijser, W., Hering, D., Kail, J. (2023) Macrophyte growth forms shift along the trophic gradient of lakes. Inland Waters, 13(3), 402–411. https://doi.org/10.1080/20442041.2023.2271307

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Researchgate
Abstract

A shift in phototrophic organisms occurs along lake trophic gradients characterized by a change from macrophyte- to phytoplankton-dominated states. Before lakes reach a turbid and phytoplankton-dominated state, shifts from meadow-forming Characeae to canopy-forming macrophyte species can occur where Characea are present, especially in oligotrophic to mesotrophic lakes with sand or gravel substrate. However, eutrophication intensity causing this shift has not previously been examined. We analysed data from 132 lakes located in Mecklenburg-Vorpommern (Germany) with a generalized linear model (GLM) and random forest (RF) models complemented with grid approximation to determine if (1) species richness of macrophytes declines along eutrophication gradients, (2) the chlorophyll a (Chl-a) concentrations above which the abundance of Characeae declines, and (3) the Chl-a concentrations above which the abundance of canopy-forming species declines. The number of macrophyte taxa declined gradually following a log-linear trend and with increasing Chl-a concentrations. Based on the RF models, the abundance of Characeae decreased abruptly at 5–13 µg L−1 Chl-a, whereas canopy-forming species showed a monotonous and slight unimodal decreasing response at 35–103 µg L−1 Chl-a. The results support the theory of shifts in growth forms along eutrophication gradients in lakes and provide, for the first time, estimates of Chl-a concentrations required for these shifts. Changes in growth forms are obvious indicators for eutrophication and can serve as an additional incentive to improve lake trophic status.


Madge Pimentel, I., Rehsen, P.M., Beermann, A.J., Leese, F., Piggott, J.J., Schmuck, S. (2023) An automated modular heating solution for experimental flow‐through stream mesocosm systems. Limnology and Oceanography: Methods, 22(3), 135-148. https://doi.org/10.1002/lom3.10596

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Abstract

Water temperature is a key environmental variable in stream ecosystems determining species distribution ranges, community composition, and ecological processes. In addition to global warming, direct anthropogenic impacts, for example through the influx of power plant cooling water or due to sun exposure after the removal of riparian vegetation, result in elevated water temperatures. However, temperature effects in stream ecosystems have mostly been tested in recirculating experimental systems, which can neither capture diurnal and seasonal variability in other environmental variables nor allow for entrainment of stream organisms. In contrast, open flow-through systems, which are constantly supplied with stream water, offer a more realistic setting for stream ecological experiments, yet are difficult to implement. Here, we outline a heating module for the purpose of differential temperature regulation in a flow-through mesocosm system by automatic control of warm water supply. We validated the functionality of the module in indoor trials as well as in an outdoor ExStream experimental mesocosm system. Furthermore, we tested the implications of different warm water temperatures for the survival of invertebrates drifting through the heating module to derive recommendations for the maximum warm water temperature for mixing with the natural water inflow. The module allows for controlled open flow-through experiments in the field and the key components are flexible and scalable. Therefore, the module can be easily integrated into existing experimental flow-through setups.


Nguyen, H.H., Welti, E.A.R., Haubrock, P.J., Haase, P. (2023) Long-term trends in stream benthic macroinvertebrate communities are driven by chemicals. Environmental Sciences Europe, 35, 108. https://doi.org/10.1186/s12302-023-00820-6

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Research gate
Abstract

Background

Recent studies indicate a partial recovery of European stream macroinvertebrate diversity. However, the key determinants shaping the overall community trends are only partly explored, owing to insufficient long-term environmental data collected in parallel with community responses. We investigate long-term trends in stream macroinvertebrate communities (i.e., taxonomic and trait composition and metrics), and explore their relationships to diverse environmental drivers (i.e., land-use, runoff, water temperature, and in-stream chemicals). We use macroinvertebrate data collected annually in spring and summer between 2007 and 2021 at four sampling sites within the Rhine-Main-Observatory Long-Term Ecological Research site. These sampling sites encompass a gradient from less-disturbed to disturbed conditions.

Results

Over time, shifts in taxonomic and trait composition and metrics indicated an improvement in environmental conditions. Long-term trends of biological trait metrics mirrored those for taxonomic metrics; for example, increases over time in taxonomic richness were paralleled by increases in functional richness and functional dispersion. Meanwhile, trends of ecological trait metrics were particularly driven by changes in environmental drivers. Land-use, water temperature, and runoff explained around 20% of the overall variance in long-term trends of macroinvertebrate communities. Water temperature and land-use played relatively equal roles in shaping taxonomic and trait composition and metric responses in spring, while water temperature emerged as the most influential driver in summer. However, when incorporating long-term chemical data as a more direct measurement of changes in land-use, the overall variance explained in macroinvertebrate community trends increased to c.a. 50% in both seasons.

Conclusions

Examining more relevant driver variables beyond land-use and climate improves insights into why biodiversity exhibits long-term trends. We call for an increase in initiatives to link biodiversity monitoring with parallel sampling of relevant environmental drivers.


Doliwa, A., Grabner, D., Sures, B., Dunthorn, M. (2023) Comparing Microsporidia-targeting primers for environmental DNA sequencing. Parasite, 30, 52. https://doi.org/10.1051/parasite/2023056 (Comparaison des amorces ciblant les Microsporidies pour le sequencage de l'ADN environnemental.)

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Research gate
Abstract

Metabarcoding is a powerful tool to detect classical, and well-known “long-branch” Microsporidia in environmental samples. Several primer pairs were developed to target these unique microbial parasites, the majority of which remain undetected when using general metabarcoding primers. Most of these Microsporidia-targeting primer pairs amplify fragments of different length of the small subunit ribosomal RNA (SSU-rRNA) gene. However, we lack a broad comparison of the efficacy of those primers. Here, we conducted in silico PCRs with three short-read (which amplify a few-hundred base pairs) and two long-read (which amplify over a thousand base pairs) metabarcoding primer pairs on a variety of publicly available Microsporidia sensu lato SSU-rRNA gene sequences to test which primers capture most of the Microsporidia diversity. Our results indicate that the primer pairs do result in slight differences in inferred richness. Furthermore, some of the reverse primers are also able to bind to microsporidian subtaxa beyond the classical Microsporidia, which include the metchnikovellidan Amphiamblys spp., the chytridiopsid Chytridiopsis typographi and the “short-branch” microsporidian Mitosporidium daphniae.


Prati, S., Enss, J., Grabner, D.S., Huesken, A., Feld, C.K., Doliwa, A., Sures, B. (2023) Possible seasonal and diurnal modulation of Gammarus pulex (Crustacea, Amphipoda) drift by microsporidian parasites. Scientific Reports, 13(1), 9474. https://doi.org/10.1038/s41598-023-36630-2

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Research gate
Abstract

In lotic freshwater ecosystems, the drift or downstream movement of animals (e.g., macroinvertebrates) constitutes a key dispersal pathway, thus shaping ecological and evolutionary patterns. There is evidence that macroinvertebrate drift may be modulated by parasites. However, most studies on parasite modulation of host drifting behavior have focused on acanthocephalans, whereas other parasites, such as microsporidians, have been largely neglected. This study provides new insight into possible seasonal and diurnal modulation of amphipod (Crustacea: Gammaridae) drift by microsporidian parasites. Three 72 h drift experiments were deployed in a German lowland stream in October 2021, April, and July 2022. The prevalence and composition of ten microsporidian parasites in Gammarus pulex clade E varied seasonally, diurnally, and between drifting and stationary specimens of G. pulex. Prevalence was generally higher in drifting amphipods than in stationary ones, mainly due to differences in host size. However, for two parasites, the prevalence in drift samples was highest during daytime suggesting changes in host phototaxis likely related to the parasite’s mode of transmission and site of infection. Alterations in drifting behavior may have important implications for G. pulex population dynamics and microsporidians’ dispersal. The underlying mechanisms are more complex than previously thought.


Deep, A., Bludau, D., Welzel, M., Clemens, S., Heider, D., Boenigk, J., Beisser, D. (2023) Natrix2 – Improved amplicon workflow with novel Oxford Nanopore Technologies support and enhancements in clustering, classification and taxonomic databases. Metabarcoding and Metagenomics, 7, e109389. https://doi.org/10.3897/mbmg.7.109389

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Research gate
Abstract

Sequencing of amplified DNA is the first step towards the generation of Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs) for biodiversity assessment and comparative analyses of environmental communities and microbiomes. Notably, the rapid advancements in sequencing technologies have paved the way for the growing utilization of third-generation long-read approaches in recent years. These sequence data imply increasing read lengths, higher error rates, and altered sequencing chemistry. Likewise, methods for amplicon classification and reference databases have progressed, leading to the expansion of taxonomic application areas and higher classification accuracy. With Natrix, a user-friendly and reducible workflow solution, processing of prokaryotic and eukaryotic environmental Illumina sequences using 16S or 18S is possible. Here, we present an updated version of the pipeline, Natrix2, which incorporates VSEARCH as an alternative clustering method with better performance for 16S metabarcoding approaches and mothur for taxonomic classification on further databases, including PR ² , UNITE and SILVA. Additionally, Natrix2 includes the handling of Nanopore reads, which entails initial error correction and refinement of reads using Medaka and Racon to subsequently determine their taxonomic classification.


Baikova, D., Boden, L., Deep, A., Doliwa, A., Hadžiomerović, U., Leese, F., Madge-Pimentel, I., Mayombo, N.A.S., Pigott, J., Prati, S., Stach, T.L., Starke, J., Vermiert, A.-M. (2023) Miniature Streams Show Scientists How Multiple Stressors Impact Our Rivers. Frontiers for Young Minds, 11, 1147094. https://doi.org/10.3389/frym.2023.1147094


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Abstract

Rivers are the lifelines of our planet. We depend on them for drinking water and food production, and they are home to many plants and animals. Unfortunately, rivers are under pressure from stressors like increasing temperatures, pollution, and habitat destruction. We often know how a single stressor impacts a river, but when more than one stressor is present at the same time, the consequences are often unpredictable. To protect our rivers now and in the future, we must understand what happens in the rivers when multiple stressors are present at the same time. However, it is difficult to understand what multiple stressors are doing to aquatic life by just observing a river or doing a laboratory experiment. In this article, you will learn how experimental miniature streams can help us to investigate the consequences of multiple stressors on rivers.


Sieber, G., Drees, F., Shah, M., Stach, T.L., Hohrenk-Danzouma, L., Bock, C., [. . .], Sures, B., Probst, A.J., Schmitdt, T.C., Beisser, D., Boenigk, J. (2023) Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater. Science of the Total Environment, 903, 167457. https://doi.org/10.1016/j.scitotenv.2023.167457

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Abstract

Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters. We aimed at assessing the impact of introducing 33 % treated wastewater into a triplicated large-scale mesocosm setup during a 10-day exposure period. Discharge of treated wastewater significantly altered the chemical signature as well as the microeukaryotic and prokaryotic diversity of the mesocosms. Non-target screening, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding detected these changes with significant covariation of the detected pattern between methods.
The 18S V9 rRNA gene metabarcoding exhibited superior sensitivity immediately following the introduction of treated wastewater and remained one of the top-performing methods throughout the study. Full-length 16S rRNA gene metabarcoding demonstrated sensitivity only in the initial hour, but became insignificant thereafter. The non-target screening approach was effective throughout the experiment and in contrast to the metabarcoding methods the signal to noise ratio remained similar during the experiment resulting in an increasing relative strength of this method. Based on our findings, we conclude that all methods employed for monitoring environmental disturbances from various sources are suitable. The distinguishing factor of these methods is their ability to detect unknown pollutants and organisms, which sets them apart from previously utilized approaches and allows for a more comprehensive perspective. Given their diverse strengths, particularly in terms of temporal resolution, these methods are best suited as complementary approaches.


Boden, L., Sieber, G., Boenigk, J. (2023) Effects of stressors on growth and competition between different cryptic taxa affiliated with Ochromonadales (Chrysophyceae). Fottea, Olomouc, 23(2), 235-245. https://doi.org/10.5507/fot.2023.003

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Abstract

Morphologically similar flagellate taxa comprise a high cryptic diversity. This diversity evolved partly through parallel evolution in several phylogenetically distinct taxa. Here we investigate the effects of heat waves and salinization on growth and competition between cryptic taxa. For this purpose, we developed specific FISH probes targeting the phylogenetic clades comprising Pedospumella encystans, Spumella rivalis, and Poteriospumella lacustris, respectively.

Exposure to salt resulted in a decreasing growth rate for all three taxa. In contrast, a sudden increase in temperature to 27 °C stimulated particularly the growth of P. lacustris. This species showed a high competitive strength and the taxon–specific responses to stressors lead to a shift of community composition. This turn–over of differently adapted cryptic species with presumably similar feeding preferences and predator–prey interactions may stabilize microbial food webs facing environmental change.


Le, T.T.Y., Becker, A., Kleinschmidt, J., Mayombo, N.A.S., Farias, L., Beszteri, S., Beszteri, B. (2023) Revealing interactions between temperature and salinity and their effects on the growth of freshwater diatoms by Empirical Modelling. Phycology, 3(4), 413-435. https://doi.org/10.3390/phycology3040028

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ResearchGate
Abstract

Salinization and warming are of increasing concern for freshwater ecosystems. Interactive effects of stressors are often studied in bifactorial, two-level experimental setups. The shape of environmental reaction norms and the position of the “control” conditions along them, however, can influence the sign and magnitude of individual responses as well as interactive effects. We empirically model binary-stressor effects in the form of three-dimensional reaction norm surfaces. We monitored the growth of clonal cultures of six freshwater diatoms, Cymbella cf. incurvata, Nitzschia linearis, Cyclotella meneghiniana, Melosira varians, Ulnaria acus, and Navicula gregaria at various temperature (up to 28 ◦C) and salinity (until the growth ceased) shock treatments.

Fitting a broad range of models and comparing them using the Akaike information criterion revealed a large heterogeneity of effects. A bell-shaped curve was often observed in the response of the diatoms to temperature changes, while their growth tended to decrease with increasing electrical conductivity. C. meneghiniana was more tolerant to temperature, whilst C. incurvata and C. meneghiniana were the most sensitive to salinity changes. Empirical modelling revealed interactive effects of temperature and salinity on the slope and the breadth of response curves. Contrasting types of interactions indicates uncertainties in the estimation by empirical modelling.


He, F., Arora, R., Mansour, I. (2023) Multispecies assemblages and multiple stressors: Synthesizing the state of experimental research in freshwaters. WIREs Water, 10(3), e1641. https://doi.org/10.1002/wat2.1641

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ResearchGate
Abstract

Recent decades have witnessed a sharp biodiversity decline in freshwaters due to multiple stressors. The presence of multiple stressors is expected to affect community structure and interactions in freshwater ecosystems, with subsequent functional consequences. We synthesized the state of experimental, manipulative multiple‐stressor studies that focused on multispecies assemblages in freshwaters. Compared to rivers and lakes, wetland and groundwater ecosystems have received much less attention in identified multiple‐stressor research.

Most of the identified studies investigated combinations of abiotic stressors (e.g., nutrients, pesticides, heavy metals, warming, altered flow and sedimentation) on microbes and invertebrates while biotic stressors and vertebrates have been largely overlooked. The responses of community structure (e.g., alpha diversity, biomass, and abundance), some community/ecosystem functions (e.g., photosynthesis and autotrophic activity, leaf litter degradation), and morphological traits like body size and growth forms were frequently investigated. We observed a clear gap in biotic interactions under multiple‐stressor conditions, which, although difficult to study, could impede a deeper mechanistic understanding of how multiple stressors affect freshwater assemblages and associated ecological processes.

Although information on ecosystem recovery pathways following restoration is critical for freshwater management, few studies were designed to provide such information, signifying the disconnections between multiple‐stressor research and environmental practice. To bridge these gaps, researchers and environmental practitioners need to work together to identify key stressors and interactions at different spatial and temporal scales and prioritize stressor management. Such collaborations will enhance the translation of multiple‐stressor research into efficient management strategies to protect and restore freshwater ecosystems. This article is categorized under: Water and Life > Stresses and Pressures on Ecosystems Water and Life > Conservation, Management, and Awareness The frequency of combinations between organisms, stressors, and ecological responses used in identified multiple‐stressor experimental studies. Only the stressor‐response linkage nodes with ≥10 counts and organism‐stressor linkage nodes with ≥5 counts were included in this diagram for purposes of clarity.


Lorenz, A.W., Kaijser, W., Acuna, V., Austnes, K., Bonada, N., Dorflinger, G., [. . .], Hering, D. (2023) Stressors affecting the ecological status of temporary rivers in the Mediterranean region. Science of the Total Environment, 903, 166254. https://doi.org/10.1016/j.scitotenv.2023.166254

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ResearchGate
Abstract

Temporary rivers are widespread in the Mediterranean region and impose a challenge for the implementation of the Water Framework Directive (WFD) and other environmental regulations. Surprisingly, an overarching analysis of their ecological status and the stressors affecting them is yet missing. We compiled data on the ecological status of 1504 temporary rivers in seven European Mediterranean region countries and related their ecological status (1) to publicly available data on pressures from the European WISE-WFD dataset, and (2) to seven more specific stressors modelled on a sub-catchment scale. More than 50 % of the temporary water bodies in the Mediterranean countries reached good or even high ecological status. In general, status classes derived from phytobenthos and macrophyte assessment were higher than those derived from the assessment of benthic invertebrates or fish.

Of the more generally defined pressures reported to the WISE-WFD database, the most relevant for temporary rivers were 'diffuse agricultural' and 'point urban waste water'. Of the modelled more specific stressors, agricultural land use best explained overall ecological status, followed by total nitrogen load, and urban land use, while toxic substances, total phosphorus load and hydrological stressors were less relevant. However, stressors differed in relevance, with total nitrogen being most important for macrophytes, and agricultural land use for phytobenthos, benthic invertebrates and fish.

For macrophytes, ecological quality increases with stressor intensity. The results underline the overarching effect of land use intensity for the ecological status of temporary water bodies. However, assessment results do not sufficiently reflect hydrological stress, most likely as the biological indicators used to evaluate these systems were designed for perennial water bodies and thus mainly target land use and nutrient impacts. We conclude that biomonitoring systems need to be adapted or newly developed to better account for the specific situation of temporary water bodies.


Grabner, D., Rothe, L.E., Sures, B. (2023) Parasites and pollutants: Effects of multiple stressors on aquatic organisms. Environmental Toxicology and Chemistry, 42(9), 1946-1959. https://doi.org/10.1002/etc.5689

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ResearchGate
Abstract

Parasites can affect their hosts in various ways, and this implies that parasites may act as additional biotic stressors in a multiple-stressor scenario, resembling conditions often found in the field if, for example, pollutants and parasites occur simultaneously. Therefore, parasites represent important modulators of host reactions in ecotoxicological studies when measuring the response of organisms to stressors such as pollutants. In the present article, we introduce the most important groups of parasites occurring in organisms commonly used in ecotoxicological studies ranging from laboratory to field investigations.

After briefly explaining their life cycles, we focus on parasite stages affecting selected ecotoxicologically relevant target species belonging to crustaceans, molluscs, and fish. We included ecotoxicological studies that consider the combination of effects of parasites and pollutants on the respective model organism with respect to aquatic host-parasite systems. We show that parasites from different taxonomic groups (e.g. Microsporidia, Monogenea, Trematoda, Cestoda, Acanthocephala, Nematoda) clearly modulate the response to stressors in their hosts.

The combined effects of environmental stressors and parasites can range from additive, antagonistic to synergistic. This review points to potential drawbacks of ecotoxicological tests if parasite infections of test organisms, especially from the field, remain undetected and unaddressed. If these parasites are not detected and quantified, their physiological effects on the host cannot be separated from the ecotoxicological effects. This may render this type of ecotoxicological test erroneous. In laboratory tests, for example to determine effect or lethal concentrations, the presence of a parasite can also have a direct effect on the concentrations to be determined and thus, on the subsequently determined security levels such as predicted no effect concentrations.


Hesse, T., Nachev, M., Khaliq, S., Jochmann, M.A., Franke, F., Scharsack, J.P., [. . .], Schmidt, T.C. (2023) A new technique to study nutrient flow in host-parasite systems by carbon stable isotope analysis of amino acids and glucose. Scientific Reports, 13(1), 1054. https://doi.org/10.1038/s41598-022-24933-9

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ResearchGate
Abstract

Stable isotope analysis of individual compounds is emerging as a powerful tool to study nutrient origin and conversion in host-parasite systems. We measured the carbon isotope composition of amino acids and glucose in the cestode Schistocephalus solidus and in liver and muscle tissues of its second intermediate host, the three-spined stickleback (Gasterosteus aculeatus), over the course of 90 days in a controlled infection experiment.

Similar linear regressions of δ13C values over time and low trophic fractionation of essential amino acids indicate that the parasite assimilates nutrients from sources closely connected to the liver metabolism of its host. Biosynthesis of glucose in the parasite might occur from the glucogenic precursors alanine, asparagine and glutamine and with an isotope fractionation of − 2 to – 3 ‰ from enzymatic reactions, while trophic fractionation of glycine, serine and threonine could be interpreted as extensive nutrient conversion to fuel parasitic growth through one-carbon metabolism.

Trophic fractionation of amino acids between sticklebacks and their diets was slightly increased in infected compared to uninfected individuals, which could be caused by increased (immune-) metabolic activities due to parasitic infection. Our results show that compound-specific stable isotope analysis has unique opportunities to study host and parasite physiology.


Gillmann, S.M., Hering, D., Lorenz, A.W. (2023) Habitat development and species arrival drive succession of the benthic invertebrate community in restored urban streams. Environmental Sciences Europe, 35, 49. https://doi.org/10.1186/s12302-023-00756-x

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ResearchGate
Abstract

Background

Urban streams are characterised by species-poor and frequently disturbed communities. The recovery of heavily polluted urban streams is challenging but the simple community structure makes recolonisation patterns more transparent. Therefore, they are generally applicable model systems for recolonisation of restored streams. Principal questions of stream restoration concern the drivers and patterns of recolonisation processes. Rarely, recolonisation of restored streams is recorded for a sufficient time to observe patterns of habitat and community development in detail. Over 10 years, we monitored benthic habitat changes and macroinvertebrate communities of eight restored sites in an urban stream network that was formerly used as an open sewer and thus, almost uninhabitable for macroinvertebrates prior to restoration. We analysed changes in environmental variables and communities with a selection of multi-variate analyses and identified indicator species in successional stages.

Results

Proportions of stony substrate and conductivity decreased over time since restoration, while the riparian vegetation cover increased along with the amount of sandy substrate. The communities fluctuated strongly after restoration but began to stabilise after around eight years. TITAN analysis identified 9 species, (e.g. the mayfly Cloeon dipterum and the beetle Agabus didymus), whose abundances decreased with time since restoration, and 19 species with an increasing abundance trend (e.g. several Trichopteran species, which colonised once specific habitats developed). Woody riparian vegetation cover and related variables were identified as major driver for changes in species abundance. In the last phase of the observation period, a dry episode resulted in complete dewatering of some sites. These temporarily dried sections were recolonised much more rapidly compared to the recolonisation following restoration.

Conclusions

Our results underline that community changes following urban stream restoration are closely linked to the evolving environmental conditions of restored streams, in particular habitat availability initialised by riparian vegetation. It takes about a decade for the development of a rich and stable community. Even in streams that were almost completely lacking benthic invertebrates before restoration, the establishment of a diverse macroinvertebrate community is possible, underlining the potential for habitat restoration in formerly heavily polluted urban areas.


Sures, B., Nachev, M., Schwelm, J., Grabner, D., Selbach, C. (2023) Environmental parasitology: stressor effects on aquatic parasites. Trends in Parasitology, 39(6), 461-474. https://doi.org/10.1016/j.pt.2023.03.005

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ResearchGate
Abstract

Environmental parasitology: stressor effects on aquatic parasites

Anthropogenic stressors are causing fundamental changes in aquatic habitats and to the organisms inhabiting these ecosystems. Yet, we are still far from understanding the diverse responses of parasites and their hosts to these environmental stressors and predicting how these stressors will affect host–parasite communities. Here, we provide an overview of the impacts of major stressors affecting aquatic ecosystems in the Anthropocene (habitat alteration, global warming, and pollution) and highlight their consequences for aquatic parasites at multiple levels of organisation, from the individual to the community level. We provide directions and ideas for future research to better understand responses to stressors in aquatic host–parasite systems.


Stach, T.L., Sieber, G., Shah, M., Simon, S.A., Soares, A., Bornemann, T.L.V., [. . .], Boenigk, J., Probst, A.J. (2023) Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater. Microbiologyopen, 12(2), e1347. https://doi.org/10.1002/mbo3.1347

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ResearchGate
Abstract

Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater

Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray–Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.


Vos, M., Hering, D., Gessner, M. O., Leese, F., Schäfer, R. B., Tollrian, R., Boenigk, J., Haase, P., Meckenstock, R., Baikova, D., Bayat, H., Beermann, A., Beißer, D., Beszteri, B., Birk, S., Boden, L., Brauer, V., Brauns, M., Buchner, D., [...] Sures, B. (2023). The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release. Science of The Total Environment, 162196. https://doi.org/10.1016/j.scitotenv.2023.162196

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ResearchGate
Abstract

The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release

Our capacity to predict trajectories of ecosystem degradation and recovery is limited, especially when impairments are caused by multiple stressors. Recovery may be fast or slow and either complete or partial, sometimes result in novel ecosystem states or even fail completely. Here, we introduce the Asymmetric Response Concept (ARC) that provides a basis for exploring and predicting the pace and magnitude of ecological responses to, and release from, multiple stressors. The ARC holds that three key mechanisms govern population, community and ecosystem trajectories. Stress tolerance is the main mechanism determining responses to increasing stressor intensity, whereas dispersal and biotic interactions predominantly govern responses to the release from stressors. The shifting importance of these mechanisms creates asymmetries between the ecological trajectories that follow increasing and decreasing stressor intensities. This recognition helps to understand multiple stressor impacts and to predict which measures will restore communities that are resistant to restoration.


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2022

Mack, L., de la Hoz, C.F., Penk, M., Piggott, J., Crowe, T., Hering, D., [. . .], Birk, S. (2022) Perceived multiple stressor effects depend on sample size and stressor gradient length. Water Research, 226, 119260. https://doi.org/10.1016/j.watres.2022.119260

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ResearchGate
Abstract

Perceived multiple stressor effects depend on sample size and stressor gradient length

Multiple stressors are continuously deteriorating surface waters worldwide, posing many challenges for their conservation and restoration. Combined effect types of multiple stressors range from single-stressor dominance to complex interactions. Identifying prevalent combined effect types is critical for environmental management, as it helps to prioritise key stressors for mitigation. However, it remains unclear whether observed single and combined stressor effects reflect true ecological processes unbiased by sample size and length of stressor gradients. Therefore, we examined the role of sample size and stressor gradient lengths in 158 paired-stressor response cases with over 120,000 samples from rivers, lakes, transitional and marine ecosystems around the world. For each case, we split the overall stressor gradient into two partial gradients (lower and upper) and investigated associated changes in single and combined stressor effects. Sample size influenced the identified combined effect types, and stressor interactions were less likely for cases with fewer samples. After splitting gradients, 40 % of cases showed a change in combined effect type, 30 % no change, and 31 % showed a loss in stressor effects. These findings suggest that identified combined effect types may often be statistical artefacts rather than representing ecological processes. In 58 % of cases, we observed changes in stressor effect directions after the gradient split, suggesting unimodal stressor effects. In general, such non-linear responses were more pronounced for organisms at higher trophic levels. We conclude that observed multiple stressor effects are not solely determined by ecological processes, but also strongly depend on sampling design. Observed effects are likely to change when sample size and/or gradient length are modified. Our study highlights the need for improved monitoring programmes with sufficient sample size and stressor gradient coverage. Our findings emphasize the importance of adaptive management, as stress reduction measures or further ecosystem degradation may change multiple stressor-effect relationships, which will then require associated changes in management strategies.


Sures, B., Nachev, M. (2022) Effects of multiple stressors in fish: how parasites and contaminants interact. Parasitology, 149(14), 1822-1828. https://doi.org/10.1017/S0031182022001172

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ResearchGate
Abstract

Interest in local environmental conditions and the occurrence and behaviour of parasites has increased over the last 3 decades, leading to the discipline of Environmental Parasitology. The aim of this discipline is to investigate how anthropogenically altered environmental factors influence the occurrence of parasites and how the combined effects of pollutants and parasites affect the health of their hosts. Accordingly, in this paper, we provide an overview of the direct and indirect effects of pollutants on the occurrence and distribution of fish parasites.

However, based on current knowledge, it is difficult to draw general conclusions about these interdependencies, as the effects of pollutants on free-living (larval) parasite stages, as well as their effects on ectoparasites, depend on the pollutant–host–parasite combination as well as on other environmental factors that can modulate the harmful effects of pollutants. Furthermore, the question of the combined effects of the simultaneous occurrence of parasites and pollutants on the physiology and health of the fish hosts is of interest.

For this purpose, we differentiate between the dominance effects of individual stressors over other, additive or synergistically reinforcing effects as well as combined antagonistic effects. For the latter, there are only very few studies, most of which were also carried out on invertebrates, so that this field of research presents itself as very promising for future investigations.


Hesse, T., Nachev, M., Khaliq, S., Jochmann, M.A., Franke, F., Scharsack, J.P., [. . .], Sures, B., Schmidt, T.C. (2022) Insights into amino acid fractionation and incorporation by compound-specific carbon isotope analysis of three-spined sticklebacks. Scientific Reports, 12(1), 11690. https://doi.org/10.1038/s41598-022-15704-7

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ResearchGate
Abstract

Interpretation of stable isotope data is of upmost importance in ecology to build sound models for the study of animal diets, migration patterns and physiology. However, our understanding of stable isotope fractionation and incorporation into consumer tissues is still limited. We therefore measured the δ¹³C values of individual amino acids over time from muscle and liver tissue of three-spined sticklebacks (Gasterosteus aculeatus) on a high protein diet.

The δ¹³C values of amino acids in the liver quickly responded to small shifts of under ± 2.0‰ in dietary stable isotope compositions on 30-day intervals. We found on average no trophic fractionation in pooled essential (muscle, liver) and non-essential (muscle) amino acids. Negative Δδ¹³C values of − 0.7 ± 1.3‰ were observed for pooled non-essential (liver) amino acids and might indicate biosynthesis from small amounts of dietary lipids. Trophic fractionation of individual amino acids is reported and discussed, including unusual Δδ¹³C values of over + 4.9 ± 1.4‰ for histidine.

Arginine and lysine showed the lowest trophic fractionation on individual sampling days and might be useful proxies for dietary sources on short time scales. We suggest further investigations using isotopically enriched materials to facilitate the correct interpretation of ecological field data.


Hedlund, B.P., Chuvochina, M., Hugenholtz, P., Konstantinidis, K.T., Murray, A.E., Palmer, M., [. . .], Probst, A., [. . .], Whitman, W.B. (2022) SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nature Microbiology, 7, 1702-1708. https://doi.org/10.1038/s41564-022-01214-9

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ResearchGate
Abstract

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.


Schneider, R., Prati, S., Grabner, D., Sures, B. (2022) First report of microsporidians in the non-native shrimp Neocaridina davidi from a temperate European stream. Diseases of Aquatic Organisms, 150, 125-130. https://doi.org/10.3354/dao03681

Related project:

ResearchGate
Abstract

First report of microsporidians in the non-native shrimp Neocaridina davidi from a temperate European stream

The release of ornamental pets outside their native range can directly or indirectly impact the recipient community, e.g. via the co-introduction of associated pathogens. However, studies on parasites associated with non-native species, in particular freshwater decapods, have focused mainly on a limited set of pathogens. Here we provide data for the first time on microsporidian parasites of the non-native ornamental shrimp Neocaridina davidi, collected in a stream in Germany. Furthermore, we confirm an ongoing range expansion of the warm-adapted N. davidi from thermally polluted colder water. In the investigated shrimps, the microsporidian parasite Enterocytozoon hepatopenaei and an unknown microsporidian isolate were detected, raising concerns about their transmission potential and pathogenicity on native crustacean species.


Whitman, W.B., Chuvochina, M., Hedlund, B.P., Hugenholtz, P., Konstantinidis, K.T., Murray, A., [. . .], Probst, A., [...], Venter, S.N. (2022) Development of the SeqCode: a proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Systematic and Applied Microbiology, 45(5), 126305-126305. https://doi.org/10.1016/J.SYAPM.2022.126305

Related project:

ResearchGate
Abstract

Development of the SeqCode: a proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yetuncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.


Prati, S., Grabner, D.S., Pfeifer, S.M., Lorenz, A.W., Sures, B. (2022) Generalist parasites persist in degraded environments: a lesson learned from microsporidian diversity in amphipods. Parasitology, 149(7), 1-10. https://doi.org/10.1017/S0031182022000452

Related projects:

ResearchGate
Abstract

Generalist parasites persist in degraded environments: a lesson learned from microsporidian diversity in amphipod

The present study provides new insight into suitable microsporidian-host associations. It relates regional and continental-wide host specialization in microsporidians infecting amphipods to degraded and recovering habitats across 2 German river catchments. It provides a unique opportunity to infer the persistence of parasites following anthropogenic disturbance and their establishment in restored rivers. Amphipods were collected in 31 sampling sites with differing degradation and restoration gradients. Specimens were morphologically (hosts) and molecularly identified (host and parasites). Amphipod diversity and abundance, microsporidian diversity, host phylogenetic specificity and continental-wide beta-specificity were investigated and related to each other and/or environmental variables. Fourteen microsporidian molecular operational taxonomic units (MOTUs), mainly generalist parasites, infecting 6 amphipod MOTUs were detected, expanding the current knowledge on the host range by 17 interactions. There was no difference in microsporidian diversity and host specificity among restored and near-natural streams (Boye) or between those located in urban and rural areas (Kinzig). Similarly, microsporidian diversity was generally not influenced by water parameters. In the Boye catchment, host densities did not influence microsporidian MOTU richness across restored and near-natural sites. High host turnover across the geographical range suggests that neither environmental conditions nor host diversity plays a significant role in the establishment into restored areas. Host diversity and environmental parameters do not indicate the persistence and dispersal of phylogenetic host generalist microsporidians in environments that experienced anthropogenic disturbance. Instead, these might depend on more complex mechanisms such as the production of resistant spores, host switching and host dispersal acting individually or conjointly.