Biomonitoring of Human Impacts in Freshwater Ecosystems

Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates

Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.

Exploring invasiveness and versatility of used microhabitats of the globally invasive Gambusia holbrooki

Non-native species can lead to severe impacts on invaded ecosystems, including the decline of ecosystem function through deleterious impacts on species diversity. The successful establishment of non-native species in new environments is the first barrier a species must overcome, ultimately depending on its ability to either cope with or adapt to local site-specific conditions. Despite the widespread distribution and ecological consequences of many freshwater invaders, site-specific and climatic preferences are often unknown. This is also the case of the Eastern mosquitofish Gambusia holbrooki, a global invader considered as a pervasive threat to endemic species. Here, we determined the ecological features and preferred site-specific conditions of G. holbrooki in Türkiye, which spans a wide range of diverse biogeographically distinct ecosystems by surveying populations from 130 localities in 2016 and 2017. Gambusia holbrooki were detected by hand-net in 48 of these sites (19 lotic, 29 lentic). It showed a preference for shallow waters with medium sized rocks, and abundances differed spatially across a latitudinal gradient and was influenced predominantly by variations in pH. The only other factors predicting its presence were low current velocities and gravel substrate, highlighting its ecological versatility in utilising a wide range of microhabitats. Bioclimatic models suggest that G. holbrooki is found in areas with a wide average annual temperature ranging from 10 to 20 °C, but with temperature not being a limiting factor to its invasion. Gambusia holbrooki shows a preference for xeric freshwater ecosystems and endorheic basins, as well as temperate coastal rivers, temperate upland rivers, temperate floodplain rivers and wetlands, and tropical and subtropical coastal rivers. These results, particularly the wide occurrence with only few limiting factors, emphasise the invasion potential of mosquitofish and should substantiate the need for localised invasive species management and conservation efforts, particularly in smaller or insular areas where mosquitofish and endemic fish species co-exist.

Potential effects of the discharge of wastewater treatment plant (WWTP) effluents in benthic communities: evidence from three distinct WWTP systems

Wastewater treatment plant (WWTP) effluents can be sources of environmental contamination. In this study, we aimed to understand whether effluents of three different WWTPs may have ecological effects in riverine recipient ecosystems. To achieve this, we assessed benthic phytobenthos and macroinvertebrate communities at three different locations relative to the effluent discharge: immediately upstream, immediately downstream and 500-m downstream the effluent discharge. Two approaches were employed: the ecological status classification as defined in the Water Framework Directive (WFD) based on biological indicators; constrained multivariate analysis to disentangle the environmental drivers (physicochemical variables and contaminants, namely metals, polycyclic aromatic hydrocarbons, pharmaceuticals, and personal care products) of ecological changes across the study sites. The results showed inconsistencies between the WFD approach and the multivariate approach, as well as between the responses of macroinvertebrates and diatoms. The WWTP effluents impacted benthic communities in a single case: macroinvertebrates were negatively affected by one of the WWTP effluents, likely by the transported pharmaceuticals (other stressors are essentially homogeneous among sites). Given the findings and the scarcity of consistent evidence on ecological impacts that WWTP effluents may have in recipient ecosystems, further research is needed towards more sustainable regulation and linked environmental protection measures.

Citizen science shows that small agricultural streams in Germany are in a poor ecological status

Agricultural pesticides, nutrients, and habitat degradation are major causes of insect declines in lowland streams. To effectively conserve and restore stream habitats, standardized stream monitoring data and societal support for freshwater protection are needed. Here, we sampled 137 small stream monitoring sites across Germany, 83 % of which were located in agricultural catchments, with >900 citizen scientists in 96 monitoring groups. Sampling was carried out according to Water Framework Directive standards as part of the citizen science freshwater monitoring program FLOW in spring and summer 2021, 2022 and 2023. The biological indicator SPEARpesticides was used to assess pesticide exposure and effects based on macroinvertebrate community composition. Overall, 58 % of the agricultural monitoring sites failed to achieve a good ecological status in terms of macroinvertebrate community composition and indicated high pesticide exposure (SPEARpesticides status class: 29 % "moderate", 19 % "poor", 11 % "bad"). The indicated pesticide pressure in streams was related to the proportion of arable land in the catchment areas (R2 = 0.23, p < 0.001). Also with regards to hydromorphology, monitoring results revealed that 65 % of the agricultural monitoring sites failed to reach a good status. The database produced by citizen science groups was characterized by a high degree of accuracy, as results obtained by citizen scientists and professionals were highly correlated for SPEARpesticides index (R2 = 0.79, p < 0.001) and hydromorphology index values (R2 = 0.72, p < 0.001). Such citizen-driven monitoring of the status of watercourses could play a crucial role in monitoring and implementing the objectives of the European Water Framework Directive, thus contributing to restoring and protecting freshwater ecosystems.

Monthly sampling reveals seasonal fine sediment fluctuations and riverine invertebrate community responses

Managing the impacts of anthropogenically enhanced deposited fine sediment levels in lotic ecosystems requires understanding of how catchment land-use changes have altered the natural sediment regime (erosion, transport, deposition) of rivers. Unfortunately, no existing studies have employed an appropriate sampling frequency over a period encompassing the full range of seasonal flow conditions expected to influence in-stream sediment dynamics. We determined the short-term (monthly) dynamics of deposited fine sediment and invertebrate communities over 12-months in 15 fourth- and fifth-order rivers draining catchments of low, medium and high land-use intensity in Southland, New Zealand to determine when and where fine sediment threatens stream health. We compared the Quorer resuspension method (suspendable inorganic sediment, SIS) and the in-stream visual sediment cover assessment method, and evaluated the effectiveness of four commonly-used invertebrate stream health metrics against their newly developed sediment-specific counterparts. Monthly variability in SIS was substantial across all land-use categories, but became more pronounced as land-use intensity increased. All 15 sites experienced a prolonged period of relatively stable flow which coincided with the largest short-term increase in SIS at 14 of the 15 sites. However, variability in SIS was not mirrored in macroinvertebrate metrics. These findings suggest that controlling inputs of fine sediment to rivers and streams will be most effective when targeted at periods of prolonged stable flow, particularly within high land-use intensity catchments. The resuspension method consistently outperformed visual estimates when considering its relationship with macroinvertebrate metrics, while sediment-specific metrics demonstrated a stronger association with fine sediment than commonly employed metrics e.g. (%EPT). We conclude that restoration/mitigation practices cannot be based solely on short-term, or even long-term, reductions in fine sediment, or on physical measures alone, but should be based on long-term recoveries of sediment-impacted invertebrate communities using concurrent measurements of both biotic and abiotic conditions.

Monitoring for the adaptive management of rivers

Monitoring for adaptive management (AM) involves collection of data with the aim of reducing uncertainty about links between human pressures (e.g. water abstraction from rivers), consequent stressors (e.g. low river flows) and environmental state (e.g. biodiversity). 'Surveillance monitoring' involves documenting trends in state, without the aim of understanding relationships between state, stressors, and pressures. Critics have highlighted that surveillance monitoring dominates monitoring investments but is not supporting AM. Decision-makers continue to be disappointed by monitoring data that are unsuitable for AM, yet designers of monitoring programs tend to make decisions that reinforce rather than reimagine the status quo. We argue that a structured, collaborative approach to objective-setting is required to break the status quo. We collaborated with regional management authorities to develop monitoring objectives and implementation strategies to support AM of New Zealand's rivers. Our collaborative approach discouraged 'failure fearing' and encouraged reimagining 'what could be' as opposed to 'what is.' Seventeen monitoring objectives were identified based on the AM requirements of national policy and regional authorities. Several objectives-particularly those arising from national policy-stretch the limits of what environmental science can currently provide. There were also strong trade-offs among objectives. We offer practical implementation strategies for overcoming the technical challenges of, and reducing trade-offs among, monitoring objectives. These strategies point to a monitoring program that contrasts strongly with one aimed at surveillance. Monitoring for AM is more complex than monitoring for surveillance, so strong leadership is required for successful implementation.

Mercury accumulation efficiency of different biomonitors in indoor environments: the case study of the Central Italian Herbarium (Florence, Italy)

Biomonitoring studies are often employed to track airborne pollutants both in outdoor and indoor environments. In this study, the mercury (Hg) sorption by three biomonitors, i.e., Pinus nigra bark, Pseudovernia furfuracea lichen, and Hypnum cupressiforme moss, was investigated in controlled (indoor) conditions. In comparison to outdoor environments, controlled conditions offer the opportunity to investigate more in detail the variables (humidity, temperature, pollutants speciation, etc.) that control Hg uptake. The biomonitors were exposed in two distinct periods of the year for 2 and 12 months respectively, in the halls of the Central Italian Herbarium (Natural History Museum of the University of Florence, Italy), which are polluted by Hg, due to past plant sample treatments. The Hg sorption trend was monitored every 3 weeks by recording: (i) the Hg content in the substrata, (ii) gaseous elemental mercury (GEM) concentrations in the exposition halls, (iii) temperature, (iv) humidity, and (v) particulate matter (PM) concentrations. At the end of the experiment, Hg concentrations in the biomonitors range from 1130 ± 201 to 293 ± 45 μg kg-1 (max-min) in barks, from 3470 ± 571 to 648 ± 40 μg kg-1 in lichens, and from 3052 ± 483 to 750 ± 127 μg kg-1 in mosses. All the biomonitors showed the highest Hg accumulation after the first 3 weeks of exposure. Mercury concentrations increased over time showing a continuous accumulation during the experiments. The biomonitors demonstrated different Hg accumulation trends in response to GEM concentrations and to the different climatic conditions (temperature and humidity) of the Herbarium halls. Barks strictly reflected the gaseous Hg pollution, while lichen and moss accumulation was also influenced by the climatic conditions of the indoor environment. Mercury bound to PM seemed to provide a negligible contribution to the biomonitors final uptake.

Establishing riverine nutrient criteria using individual taxa thresholds

Nutrient enrichment is one of the most pervasive impacts on aquatic ecosystems globally. Approaches to establish nutrient criteria that safeguard aquatic ecosystem health are highly variable and, in many instances, criteria are derived from correlations between in-situ nutrient concentrations and biological indices. Summarising entire assemblages with a single index can result in a substantial loss of information and potentially weaker relationships. In this study, we compared the derivation of nutrient criteria using biological indices and those from individual taxa for rivers and streams in New Zealand. Random forest models, including nutrient concentrations, were built to predict two biological indices and individual taxa across New Zealand's river monitoring network. For all acceptable models, the response of the biological indices and individual taxa to increasing Dissolved Inorganic Nitrogen (DIN) and Dissolved Reactive Phosphorus (DRP) were then predicted for every river reach across the nation, and nutrient concentrations that protected 80% of taxa were then identified. Models for the biological indices were poor but were good for most of the taxa, with nutrient concentrations almost always being the most influential factor. To ensure persistence of at least 80% of the taxa within a river reach, we estimated that DIN (Dissolved Inorganic Nitrogen) concentrations would need to be below 0.57-1.32 mg/L, and DRP (Dissolved Reactive Phosphorus) concentrations below 0.019-0.033 mg/L, depending on the river type. In general, high order, low slope rivers and streams required more stringent nutrient criteria than steep, low order streams. The link between nutrient concentrations and biological indices were weak and likely suffer from the loss of information from summarising an entire assemblage into a single numeric. We consider that the derivation of nutrient criteria for waterways should also examine the individual relationships with the taxa in a river system to establish protection for a desired proportion of taxa.

Evidence of biological recovery from gross pollution in English and Welsh rivers over three decades

Uncertainty around the changing ecological status of European rivers reflects an evolving array of anthropogenic stressors, including climate change. Although previous studies have revealed some recovery from historical pollution in the 1990s and early-2000s, there are contrasting trends among pollutants across Europe and recovery may have stalled or been reversed. To provide more contemporary evidence on trends and status, here we investigate changes in English and Welsh river macroinvertebrate communities over almost 30 years (1991-2019) using a network of nearly 4000 survey locations. Analysis comprised: i) trends in taxonomic and functional richness, community composition and ecological traits, ii) gains, losses and turnover of taxa, and the overall homogeneity of macroinvertebrate communities nationally, and iii) an exploration of how temporal trends varied with catchment characteristics. Taxonomic richness increased, primarily in the 1990s, whilst a shift towards pollution-sensitive taxa continued throughout the study period, accompanied by a growing prevalence in traits such as preferences for fast-flowing conditions, coarser substrata, and 'shredding' or 'scraping' feeding strategies. Changes consistent with improvement occurred in both urbanised and agricultural catchments, but were more pronounced in urban rivers as they gained pollution sensitive taxa that were otherwise more prevalent in rural rivers. Overall, these results indicate continuing biological recovery from organic pollution, consistent with national scale trends in water quality. Results reemphasise the importance of looking at multiple facets of diversity, with periods of near-constant richness disguising changes in taxonomic and functional composition. Whilst this national-scale picture is broadly positive, we highlight the need to investigate more local variations or pollutants that depart from this aggregate picture.

Scaling of biological rates with body size as a backbone in the assembly of metacommunity biodiversity

The dispersal-body mass association has been highlighted as a main determinant of biodiversity patterns in metacommunities. However, less attention has been devoted to other well-recognized determinants of metacommunity diversity: the scaling in density and regional richness with body size. Among active dispersers, the increase in movement with body size may enhance local richness and decrease β-diversity. Nevertheless, the reduction of population size and regional richness with body mass may determine a negative diversity-body size association. Consequently, metacommunity assembly probably emerges from a balance between the effect of these scalings. We formalize this hypothesis by relating the exponents of size-scaling rules with simulated trends in α-, β- and γ-diversity with body size. Our results highlight that the diversity-body size relationship in metacommunities may be driven by the combined effect of different scaling rules. Given their ubiquity in most terrestrial and aquatic biotas, these scaling rules may represent the basic determinants-backbone-of biodiversity, over which other mechanisms operate determining metacommunity assembly. Further studies are needed, aimed at explaining biodiversity patterns from functional relationships between biological rates and body size, as well as their association with environmental conditions and species interactions.

Macrophyte communities as bioindicator of stormwater pollution in rivers: a quantitative analysis

Macrophytes are one of the important indicators used in assessing the anthropic impact on aquatic ecosystems. The structure of macrophyte communities of two rivers were compared by species composition, dominant species and projective cover using statistical methods. It is shown that the influence of storm runoff on these rivers is manifested in the form of a change in the dominant species composition. Based on the statistical analysis carried out, it can be argued that, despite the peculiarities of the flora composition of each of the rivers, the influence of storm runoffs largely neutralizes this specificity, determining the situation in local areas immediately below the runoff. In the area of the effluent discharge the dominance of individual species and an increase in the area overgrown with macrophytes was observed. In the area of stormwater discharge on the Psel River, species were usually present: Nuphar lutea, Ceratophyllum demersum, Myriophyllum spicatum and on the Bystrica River-Glyceria maxima, Sagitaria sagittiformis, Stuckenia pectinata and Potamogeton crispus. The use of the NMDS method has been found to provide good insight into the structural rearrangements in macrophyte communities affected by runoff from stormwater systems.

Differences in Phytobenthic Diatom Community between Natural and Channelized River Sections

The structure of phytobenthic diatom communities was studied to reveal differences between natural and channelized river sections in Slovenia. As part of the national monitoring of surface waters, samples of phytobenthos were collected at 85 sites throughout the country according to standard protocols. At the same time, basic environmental parameters were also assessed. Trophic (TI) and saprobic (SI) indices were calculated based on diatoms and other algae, while diversity indices and gradient analyses were performed only for the diatom community. The results showed that channelized rivers harbor significantly more diverse benthic diatom communities than natural sections, mainly due to the significantly higher number of motile diatom taxa that are able to take advantage of more nutrient-rich and less-shaded river sections because of their high adaptability. Selected environmental parameters explained 34% of the variability in diatom community structure when taxa were classified into ecological types. The removal of Achnanthidium minutissimum yielded clearer results (24.1%) than the total species matrix (22.6%). Therefore, we suggest excluding this taxon from calculations of TI, SI, or other indices when it is determined as A. minutissimum complex, because A. minutissimum complex was most abundant in both types of reaches in our study and has a wide ecological amplitude, which reduces the indicative power of the diatom community in the evaluation of environmental conditions and ecological status.

Using invertebrate functional traits to improve flow variability assessment within European rivers

Rivers are among the most threatened ecosystems worldwide and are experiencing rapid biodiversity loss. Flow alteration due to climate change, water abstraction and augmentation is a severe stressor on many aquatic communities. Macroinvertebrates are widely used for biomonitoring river ecosystems although current taxonomic approaches used to characterise ecological responses to flow have limitations in terms of generalisation across biogeographical regions. A new macroinvertebrate trait-based index, Flow-T, derived from ecological functional information (flow velocity preferences) currently available for almost 500 invertebrate taxa at the European scale is presented. The index was tested using data from rivers spanning different biogeographic and hydro-climatic regions from the UK, Cyprus and Italy. The performance of Flow-T at different spatial scales and its relationship with an established UK flow assessment tool, the Lotic-invertebrate Index for Flow Evaluation (LIFE), was assessed to determine the transferability of the approach internationally. Flow-T was strongly correlated with the LIFE index using both presence-absence and abundance weighted data from all study areas (r varying from 0.46 to 0.96). When applied at the river reach scale, Flow-T was effective in identifying communities associated with distinct mesohabitats characterised by their hydraulic characteristics (e.g., pools, riffles, glides). Flow-T can be derived using both presence/absence and abundance data and can be easily adapted to varying taxonomic resolutions. The trait-based approach facilitates research using the entire European invertebrate fauna and can potentially be applied in regions where information on taxa-specific flow velocity preferences is not currently available. The inter-regional and continental scale transferability of Flow-T may help water resource managers gauge the effects of changes in flow regime on instream communities at varying spatial scales.

Relationships between Physico-Chemical Parameters and Taxonomic Structure of Benthic Macroinvertebrate Assemblages in Streams of West Cameroon

Tropical rivers are strongly influenced by stormwaters, pollutants and agro-pastoral activities. These systems are no longer able to maintain their native biota. Therefore, it seems important to understand how biological assemblages are driven by environmental gradients at different spatial scales. However, information on the relationships between the distribution of aquatic macroinvertebrates and environmental variables remains scarce in Cameroon. To improve our knowledge on the drivers of such distributions, a study was carried out at 11 contrasted sites from three catchments located in West Cameroon. This study aimed at understanding the spatio-temporal variations of 19 taxonomic metrics calculated for the benthic macroinvertebrate assemblages of these sites sampled during 13 months, concurrently with physico-chemical analyses of water quality. Two hundred and twelve taxa were caught. Diptera(rf-S), Shannon-Wiener diversity, 1–GOLD, total richness, Pielou evenness and Heteroptera(rf-S) revealed their high ability to respond to anthropogenic pressures or disturbances. Conductivity, water temperature, dissolved oxygen, nitrates, total hardness and alkalinity were identified as the main physico-chemical drivers of the taxonomic structure of benthic assemblages. These results will allow further exploration of the implementation of a tool for monitoring the ecological quality of West Cameroon rivers.

Activity, boldness and schooling in freshwater fish are affected by river salinization

Rivers are experiencing increasing anthropogenic pressures and salinity has shown to affect freshwater fish behaviour, potentially disrupting ecological processes. In this study, the aim was to determine the sub-lethal effects of salinization on freshwater fish behaviour, using a widespread native cyprinid species, the Iberian barbel (Luciobarbus bocagei) as the model species. Behavioural trials in a mesocosms setting were performed to assess the effects of three levels of a salinity gradient - control (no salt added to the water, 0.8 mS/cm), low (9 mS/cm), and high concentration (18 mS/cm) - on fish routine activity, shoal cohesion and boldness. Upon increasing the salinity levels in the flume-channels, fish showed a significant reduction on their i) swimming activity (76% of searching behaviour in the control vs. 57% in high salinity), and ii) shoal cohesion (0.95 shoal cohesion ratio in the control vs. 0.76 in high salinity), while iii) an increase of bolder individuals, measured by a higher number of attempts to escape the altered environment (106 total jumps in the control vs. 262 in high salinity), was simultaneously observed. Behavioural changes in fish can reflect shifts in ecological condition. Thus, the behavioural responses of fish caused by salinization stress should be further researched, in addition to the interaction with other environmental stressors, in order to understand the true scope of the consequences of salinization for fish species.

Monitoring and Management of Inland Waters: Insights from the Most Inhabited Italian Region

Monitoring of freshwaters allows the detection of the impacts of multiple anthropic uses and activities on aquatic ecosystems, and an eco-sustainable management of natural resources could limit these impacts. In this work, we highlighted two main issues affecting inland waters, referring to findings from the most inhabited Italian region (Lombardy, approximately 10 M inhabitants): the first issue is lake pollution by old generation pesticides, the second is river development for hydropower. In both cases, some management strategies reducing the anthropic impacts on freshwaters were discussed: organic farming and biocontrol as an alternative to diffuse pollution by agrochemicals; environmental flows and controlled sediment flushing operations to limit the hydropower impact on rivers. Although the two mentioned issues were discussed separately in this paper, the management of water resources should be carried out in a comprehensive way, accounting for the multiple impacts affecting freshwater ecosystems, including those related to the climate changes.

Assessing the feasibility and value of employing an ecosystem services approach in chemical environmental risk assessment under the Water Framework Directive

The feasibility and added value of an ecosystem services approach in retrospective environmental risk assessment were evaluated using a site-specific case study in a lowland UK river. The studied water body failed to achieve good ecological status temporarily in 2018, due in part to the exceedance of the environmental quality standard (annual average EQS) for zinc. Potential ecosystem service delivery was quantified for locally prioritised ecosystem services: regulation of chemical condition; maintaining nursery populations and habitats; recreational fishing; nature watching. Quantification was based on observed and expected taxa or functional groups within WFD biological quality elements, including macrophytes, benthic macroinvertebrates and fish, and on published functional trait data for constituent taxa. Benthic macroinvertebrate taxa were identified and enumerated before, during and after zinc EQS exceedance, enabling a generic retrospective risk assessment for this biological quality element, which was found to have good ecosystem service potential. An additional targeted risk assessment for zinc was based on laboratory-based species sensitivity distributions normalised using biotic-ligand modelling to account for site-specific, bioavailability-corrected zinc exposure. Risk to ecosystem services for diatoms (microalgae) was found to be high, while risks for benthic macroinvertebrates and fish were found to be low. The status of potential ecosystem service delivery (ESD) by fish was equivalent to high ecological status defined under the WFD, while ESD was higher for benthic macroinvertebrates than defined by WFD methods. The illustrated ecosystem services approach uses readily available data and adds significantly to the taxonomic approach currently used under the WFD by using functional traits to evaluate services that are prioritised as being important in water bodies. The main shortcomings of the illustrated approach were lack of: representation of bacteria and fungi; WFD predicted species lists for diatoms and macrophytes; site-specific functional trait data required for defining actual (rather than potential) ecosystem service delivery.

Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring

Traditional environmental biomonitoring approaches have limitations in terms of species detectability and their capacity to account for spatial and temporal variation. Furthermore, as invasive techniques they can be harmful to individual organisms, populations and habitats. The application of non-invasive sampling methods that extract, isolate and identify nucleic acid sequences (i.e. DNA, RNA) from environmental matrices have significant potential for complementing, or even ultimately replacing, current methods of biological environmental assessment. These environmental DNA (eDNA) and environmental RNA (eRNA) techniques increase spatial and temporal acuity of monitoring, and in the case of the latter, may provide functional information regarding the health of individuals, and thus ecosystems. However, these assessments require robust analysis of factors such as the detectability and specificity of the developed assays. The presented work highlights the current and future uses of nucleic acid-based biomonitoring regimes, with a focus on fish and aquatic invertebrates and their utility for water quality, biodiversity and species-specific monitoring. These techniques are compared to traditional approaches, with a particular emphasis on the potential insights that could be provided by eRNA analysis, including the benefits of microRNAs as assay targets.

Eutrophication causes invertebrate biodiversity loss and decreases cross-taxon congruence across anthropogenically-disturbed lakes

Eutrophication is a major problem currently impacting many surface water ecosystems. Impacts of increased nutrient concentrations on biodiversity may differ between different scales, different organism groups, and different trophic states. Surveys at different spatial scales have suggested that biodiversity of different taxa may exhibit significant cross-taxon congruence. In our study, we examined the diversity of zooplankton and zoobenthos across 261 lakes in the Lake Taihu watershed, an area that is undergoing a severe eutrophication process. We tested the cross-taxon congruence in species richness and Shannon-Wiener diversity between zooplankton and zoobenthos along a nutrient gradient across the lakes. Our findings were consistent with the intermediate disturbance hypothesis, considering nutrient input as the disturbance. Also, we found significant cross-taxon congruence between zooplankton and zoobenthos diversities. Our results confirmed that excess nutrient levels resulted in diversity loss and community simplification. Zoobenthos were more sensitive to nutrient increases compared with zooplankton, which decreased cross-taxon congruence because these organism groups did not respond similarly to the anthropogenic disturbance.

A Review on Atmospheric Analysis Focusing on Public Health, Environmental Legislation and Chemical Characterization

Atmospheric pollution has been considered one of the most important topics in environmental science once it can be related to the incidence of respiratory diseases, climate change, and others. Knowing the composition of this complex and variable mixture of gases and particulate matter is crucial to understand the damages it causes, help establish limit levels, reduce emissions, and mitigate risks. In this work, the current scenario of the legislation and guideline values for indoor and outdoor atmospheric parameters will be reviewed, focusing on the inorganic and organic compositions of particulate matter and on biomonitoring. Considering the concentration level of the contaminants in air and the physical aspects (meteorological conditions) involved in the dispersion of these contaminants, different approaches for air sampling and analysis have been developed in recent years. Finally, this review presents the importance of data analysis, whose main objective is to transform analytical results into reliable information about the significance of anthropic activities in air pollution and its possible sources. This information is a useful tool to help the government implement actions against atmospheric air pollution.

Which Is More Toxic? Evaluation of the Short-Term Toxic Effects of Chlorpyrifos and Cypermethrin on Selected Biomarkers in Common Carp (Cyprinus carpio, Linnaeus 1758)

The general aim of this study was to investigate the negative short-term effects of different concentrations of chlorpyrifos (CPF) and cypermethrin (CYP), based on the EU legislation (MAC-EQS) in common carp (Cyprinus carpio Linnaeus, 1758) under laboratory conditions and to compare their toxicity. The fish were exposed to the pesticides for 96 h and then different histological and biochemical biomarkers were investigated in the gills and liver, and bioaccumulation analyses were conducted. The chemical studies showed increased pesticide concentrations in the gills as the first site for pollutants compared to the liver at the 96th hour. In addition, the histological analyses showed severe alterations in the gills and liver after exposure to both tested pesticides. In the gills, we found mainly intense proliferative and, to a lesser extent, degenerative changes and alterations in the circulatory system, such as necrosis and vasodilation. In the liver, regressive and progressive lesions, as well as circulatory disturbances and inflammation, were observed. The regressive lesions showed a higher degree of expression compared to the other changes. Furthermore, we found altered enzymatic activities—catalase, glutathione reductase, and glutathione peroxidase—in the liver, compared to the control. Overall, both tested pesticides impacted the studied biomarkers in common carp, even at concentrations lower than those permitted by law. However, the results of the comparative analysis showed a relatively higher toxicity of CYP compared to CPF in the fish. Still, questions persist as to whether the observed changes are adaptive or entirely destructive. To avoid any danger or risk, these pesticides must be applied cautiously, especially near water bodies.

Mycoplankton Biome Structure and Assemblage Processes Differ Along a Transect From the Elbe River Down to the River Plume and the Adjacent Marine Waters

Rivers are transport systems and supply adjacent ecosystems with nutrients. They also serve human well-being, for example as a source of food. Microorganism biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that fungi are key players in freshwater nutrient cycling and food webs, data on planktonic fungi of streams with higher stream order are scarce. This study aims to fill this knowledge gap by a fungi-specific 18S ribosomal RNA (rRNA) gene tag sequencing approach, investigating mycoplankton diversity in the Elbe River along a transect from shallow freshwater, to the estuary and river plume down to the adjacent marine waters (sections of seventh stream order number). Using multivariate analyses and the quantitative process estimates (QPEs) method, questions (i) of how mycoplankton communities as part of the river continuum change along the transect, (ii) what factors, spatial and environmental, play a role, and (iii) what assembly processes, such as selection or dispersion, operate along the transect, were addressed. The partitioning of mycoplankton communities into three significant distant biomes was mainly driven by local environmental conditions that were partly under spatial control. The assembly processes underlying the biomes also differed significantly. Thus, variable selection dominated the upstream sections, while undominated processes like ecological drift dominated the sections close to the river mouth and beyond. Dispersal played a minor role. The results suggest that the ecological versatility of the mycoplankton communities changes along the transect as response, for example, to a drastic change from an autotrophic to a heterotrophic system caused by an abrupt increase in the river depth. Furthermore, a significant salinity-dependent occurrence of diverse basal fungal groups was observed, with no clade found exclusively in marine waters. These results provide an important framework to help understand patterns of riverine mycoplankton communities and serve as basis for a further in-depth work so that fungi, as an important ecological organism group, can be integrated into models of, e.g., usage-balance considerations of rivers.

Agricultural activities compromise ecosystem health and functioning of rivers: Insights from multivariate and multimetric analyses of macroinvertebrate assemblages

Agricultural activities often lead to nutrient enrichment and habitat modification in rivers, possibly altering macroinvertebrate assemblages and hence ecosystem functioning. For the sake of environmental management and conservation, therefore, assessing the impacts of agricultural activities becomes indispensable, especially when these activities are predicted to be intensified in the future. In this study, the plain river network in the Lake Chaohu Basin was chosen to examine how agricultural activities influence the functioning of rivers by assessing land use, water quality, habitat condition and macroinvertebrate assemblages, followed by calculating the macroinvertebrate-based multimetric index (MMI) to indicate overall ecosystem health of the rivers. We found that agricultural activities lowered the diversity of macroinvertebrates (e.g. total number of taxa and Simpson index) primarily due to elevated ammonium concentrations in water and reduced microhabitat types, thereby impairing the habitat integrity and nutrient cycling of rivers. The macroinvertebrate-based MMI was positively correlated with increasing habitat quality but negatively with increasing nutrient concentrations, suggesting its high reliability for indicating the impacts of agricultural activities, which was further substantiated by classification and regression tree (CART) analysis. We recommend analyzing macroinvertebrate assemblages using both multivariate and multimetric approaches to offer a more comprehensive evaluation of the impacts of agricultural activities on ecosystem health. Some environmental (COD_Mn, NH₄⁺-N and PO₄^3--P) and biological parameters (total number of taxa), however, can be used as good proxies for MMI, when time and resources for gathering information to develop MMI are limited.

Setting Priorities in River Management Using Habitat Suitability Models

Worldwide river systems are under pressure from human development. River managers need to identify the most important stressors in a stream basin, to propose effective management interventions for river restoration. In the European Union, the Water Framework Directive proposes the ecological status as the management endpoint for these interventions. Many decision support tools exist that use predictive water quality models to evaluate different river management scenarios, but only a few consider a river’s ecological status in this analysis explicitly. This paper presents a novel method, which combines abiotic monitoring data and biological monitoring data, to provide information and insight on why the ecological status does not reach the good status. We use habitat suitability models as a decision support tool, which can identify the most important stressors in river systems to define management scenarios. To this end, we disassemble the ecological status into its individual building blocks, i.e., the community composition, and we use habitat suitability models to perform an ecological gap analysis. In this paper, we present our method and its underlying ecological concepts, and we illustrate its benefits by applying the method on a regional level for Flanders using a biotic index, the Multimetric Macroinvertebrate Index Flanders (MMIF). To evaluate our method, we calculated the number of correctly classified instances (CCI = 47.7%) and the root-mean-square error (RMSE = 0.18) on the MMIF class and the MMIF value. Furthermore, there is a monotonic decreasing relationship between the results of the priority classification and the ecological status expressed by the MMIF, which is strengthened by the inclusion of ecological concepts in our method (Pearson’s R2 −0.92 vs. −0.87). In addition, the results of our method are complementary to information derived from the legal targets set for abiotic variables. Thus, our proposed method can further optimize the inclusion of monitoring data for the sake of sustainable decisions in river management.

Determination of Adenylate Nucleotides in Amphipod Gammarus fossarum by Ion-Pair Reverse Phase Liquid Chromatography: Possibilities of Positive Pressure Micro-Solid Phase Extraction

Adenine nucleotides—adenosine monophosphate, diphosphate, and triphosphate—are of utmost importance to all living organisms, where they play a critical role in the energy metabolism and are tied to allosteric regulation in various regulatory enzymes. Adenylate energy charge represents the precise relationship between the concentrations of adenosine monophosphate, diphosphate, and triphosphate and indicates the amount of metabolic energy available to an organism. The experimental conditions of adenylate extraction in freshwater amphipod Gammarus fossarum are reported here for the first time and are crucial for the qualitative and quantitative determination of adenylate nucleotides using efficient and sensitive ion-pair reverse phase LC. It was shown that amphipod calcified exoskeleton impeded the neutralization of homogenate. The highest adenylate yield was obtained by homogenization in perchloric acid and subsequent addition of potassium hydroxide and phosphate buffer to achieve a pH around 11. This method enables separation and accurate detection of adenylates. Our study provides new insight into the complexity of adenylate extraction and quantification that is crucial for the application of adenylate energy charge as a confident physiological measure of environmental stress and as a health index of G. fossarum.

How to Assess the Ecological Status of Highly Humic Lakes? Development of a New Method Based on Benthic Invertebrates

Highly humic lakes are typical for the boreal zone. These unique ecosystems are characterised as relatively undisturbed habitats with brown water, high acidity, low nutrient content and lack of macrophytes. Current lake assessment methods are not appropriate for ecological assessment of highly humic lakes because of their unique properties and differing human pressures acting on these ecosystems. This study proposes a new approach suitable for the ecological status assessment of highly humic lakes impacted by hydrological modifications. Altogether, 52 macroinvertebrate samples from 15 raised bog lakes were used to develop the method. The studied lakes are located in the raised bogs at the central and eastern parts of Latvia. Altered water level was found as the main threat to the humic lake habitats since no other pressures were established. A multimetric index based on macroinvertebrate abundance, littoral and profundal preferences, Coleoptera taxa richness and the Biological Monitoring Working Party (BMWP) Score is suggested as the most suitable tool to assess the ecological quality of the highly humic lakes.

Assessing mining impacts: The influence of background geochemical conditions on diatom and macroinvertebrate communities in subarctic streams

Mining has changed landscapes locally in northern Fennoscandia and there is an increasing pressure for exploitation of the remaining mineral deposits of the region. Mineral deposits, even if unmined, can strongly influence stream water chemistry, stream biological communities and the ability of organisms to tolerate stressors. Using data sampled from six mining areas with three active (gold and chrome), two closed (gold) and one planned mine (phosphate), we examined how mineral deposits and mining influence water chemistry and diatom and macroinvertebrate communities in subarctic streams in Finnish Lapland. We supplemented the data by additional samples compiled from databases and further assessed how variation in background geological conditions influences bioassessments of the impacts arising from mining. We found that water specific conductivity was elevated in our study streams draining through catchments with a high mineral potential. Mining effects were mainly seen as increased concentration of nitrogen. Influence of mineral deposits was detected in composition of diatom and macroinvertebrate communities, but communities in streams in areas with a high mineral potential were as diverse as those in streams in areas with a low mineral potential. Mining impacts were better detected for diatoms using a reference condition based on sites with a high than low mineral potential, while for macroinvertebrates, the responses were generally less evident, likely because of only minor effects of mining on water chemistry. Community composition and frequencies of occurrence of macroinvertebrate taxa were, however, highly similar between mine-influenced streams and reference streams with a high potential for minerals indicating that the communities are strongly structured by the natural influence of mineral deposits. Incorporating geochemistry into the reference condition would likely improve bioassessments of both taxonomic groups. Replicated monitoring in potentially impacted sites and reference sites would be the most efficient framework for detecting environmental impacts in streams draining through mineral-rich catchments.

The influence of nutrient enrichment on riverine food web function and stability

Nutrient enrichment of rivers and lakes has been increasing rapidly over the past few decades, primarily because of agricultural intensification. Although nutrient enrichment is known to drive excessive algal and microbial growth, which can directly and indirectly change the ecological community composition, the resulting changes in food web emergent properties are poorly understood. We used ecological network analysis (ENA) to examine the emergent properties of 12 riverine food webs across a nutrient enrichment gradient in the Manawatu, New Zealand. We also derive Keystone Sensitivity Indices to explore whether nutrients change the trophic importance of species in a way that alters the resilience of the communities to further nutrient enrichment or floods. Nutrient enrichment resulted in communities composed of energy inefficient species with high community (excluding microbes) respiration. Community respiration was several times greater in enriched communities, and this may drive hypoxic conditions even without concomitant changes in microbial respiration. Enriched communities exhibited weaker trophic cascades, which may yield greater robustness to energy flow loss. Interestingly, enriched communities were also more structurally and functionally affected by species sensitive to flow disturbance making these communities more vulnerable to floods.

Gene expression response of the alga Fucus virsoides (Fucales, Ochrophyta) to glyphosate solution exposure

Fucus virsoides is an ecologically important canopy-forming brown algae endemic to the Adriatic Sea. Once widespread in marine coastal areas, this species underwent a rapid population decline and is now confined to small residual areas. Although the reasons behind this progressive disappearance are still a matter of debate, F. virsoides may suffer, like other macroalgae, from the potential toxic effects of glyphosate-based herbicides. Here, through a transcriptomic approach, we investigate the molecular basis of the high susceptibility of this species to glyphosate solution, previously observed at the morphological and eco-physiological levels. By simulating runoff event in a factorial experiment, we exposed F. virsoides to glyphosate (Roundup® 2.0), either alone or in association with nutrient enrichment, highlighting significant alterations of gene expression profiles that were already visible after three days of exposure. In particular, glyphosate exposure determined the near-complete expression shutdown of several genes involved in photosynthesis, protein synthesis and stress response molecular pathways. Curiously, these detrimental effects were partially mitigated by nutrient supplementation, which may explain the survival of relict population in confined areas with high nutrient inputs.

Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management

Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology - the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.

Current and Future Ecological Status Assessment: A New Holistic Approach for Watershed Management

The Paiva River catchment, located in Portugal, integrates the Natura 2000 network of European Union nature protection areas. Resorting to topography, climate and land-use data, a semi-distributed hydrological model (Hydrological Simulation Program–FORTRAN) was run in order to simulate the hydrological cycle of the river and its tributaries. The model was calibrated over a 25-year period and validated within a 31-year period. Its performance was verified by comparing the recorded and simulated daily flows. The values of the Nash–Sutcliffe coefficient of efficiency of 0.95 and 0.76, and coefficient of determination of 0.95 and 0.82, were achieved for calibration and validation, respectively, thus showing a quite satisfactory model performance. Subsequently, the climate change impacts on temperature and precipitation, as well as their extremes, and on the flowrates were also assessed for a future period (2041–2070) under two anthropogenic forcing scenarios (representative concentration pathways 4.5 and 8.5). A procedure for selecting the most relevant metrics for assessing the ecological condition of the Paiva River was developed based upon a set of 52 invertebrate families sampled. Correspondence analyses were carried out for biological datasets (traits/metrics) with physicochemical and land use/land cover matrices separately. Out of all variables, water quality and flow and agriculture land use explained most of the variance observed. The integrated analysis undertaken in the present study is an important advance when compared to previous studies and it provides key information to stakeholders and decision-makers, particularly when planning suitable adaptation measures to cope with changing climates in the forthcoming decades.

Use of Aquatic Biota to Detect Ecological Changes in Freshwater: Current Status and Future Directions

Freshwater ecosystems have been severely damaged worldwide by a multitude of human pressures, such as pollution, nutrient enrichment, damming or overexploitation, and this has been more intense over the past five decades. It is therefore important that the impacts of such stressors can be effectively detected, monitored and assessed in order to provide adequate legislative tools and to protect and restore freshwater ecosystems. The use of aquatic biota to detect, measure and track changes in the environment is often known as freshwater biomonitoring and is based on the premise that the presence or absence of biotic assemblages at a given site reflects its degree of environmental quality. For over a century, since the early pollution-oriented indicators, freshwater monitoring has been developing and testing progressively more complex indicator systems, and increasing the plethora of pressures addressed, using different biological groups, such as benthic macroinvertebrates, macrophytes, fish, phytoplankton and phytobenthos. There is an increasing demand for precision and accuracy in bioassessment. In this Special Issue, five high-quality papers were selected and are briefly presented herein, that cover a wide range of issues and spatial contexts relevant to freshwater biomonitoring.

Assessing the Benefits of Forested Riparian Zones: A Qualitative Index of Riparian Integrity Is Positively Associated with Ecological Status in European Streams

Developing a general, predictive understanding of ecological systems requires knowing how much structural and functional relationships can cross scales and contexts. Here, we introduce the CROSSLINK project that investigates the role of forested riparian buffers in modified European landscapes by measuring a wide range of ecosystem attributes in stream-riparian networks. CROSSLINK involves replicated field measurements in four case-study basins with varying levels of human development: Norway (Oslo Fjord), Sweden (Lake Mälaren), Belgium (Zwalm River), and Romania (Argeş River). Nested within these case-study basins include multiple, independent stream-site pairs with a forested riparian buffer and unbuffered section located upstream, as well as headwater and downstream sites to show cumulative land-use impacts. CROSSLINK applies existing and bespoke methods to describe habitat conditions, biodiversity, and ecosystem functioning in aquatic and terrestrial habitats. Here, we summarize the approaches used, detail protocols in supplementary materials, and explain how data is applied in an optimization framework to better manage tradeoffs in multifunctional landscapes. We then present results demonstrating the range of riparian conditions present in our case-study basins and how these environmental states influence stream ecological integrity with the commonly used macroinvertebrate Average Score Per Taxon (ASPT) index. We demonstrate that a qualitative index of riparian integrity can be positively associated with stream ecological status. This introduction to the CROSSLINK project shows the potential for our replicated study with its panoply of ecosystem attributes to help guide management decisions regarding the use of forested riparian buffers in human-impacted landscapes. This knowledge is highly relevant in a time of rapid environmental change where freshwater biodiversity is increasingly under pressure from a range of human impacts that include habitat loss, pollution, and climate change.

Disentangling the Effects of Multiple Stressors on Large Rivers Using Benthic Invertebrates—A Study of Southeastern European Large Rivers with Implications for Management

Predicting anthropogenic actions resulting in undesirable changes in aquatic systems is crucial for the development of effective and sustainable water management strategies. Due to the co-occurrence of stressors and a lack of appropriate data, the effects on large rivers are difficult to elucidate. To overcome this problem, we developed a partial canonical correspondence analyses (pCCA) model using 292 benthic invertebrate taxa from 104 sites that incorporated the effects of three stressors groups: hydromorphology, land use, and water quality. The data covered an environmental gradient from near-natural to heavily altered sites in five large rivers in Southeastern Europe. Prior to developing the multi-stressor model, we assessed the importance of natural characteristics on individual stressor groups. Stressors proved to be the dominant factors in shaping benthic invertebrate assemblages. The pCCA among stressor-groups showed that unique effects dominated over joint effects. Thus, benthic invertebrate assemblages were suitable for disentangling the specific effect of each of the three stressor groups. While the effects of hydromorphology were dominant, both water quality and land use effects were nearly equally important. Quantifying the specific effects of hydromorphological alterations, water quality, and land use will allow water managers to better understand how large rivers have changed and to better define expectations for ecosystem conditions in the future.

An Assessment of Self-Purification in Streams

The territory of Lithuania is characterized by a prevailing moisture excess, therefore in order to timely remove excess water from arable lands, the drainage systems have long been installed. In order to drain excess water people used to dig trenches, to regulate (deepen or straighten) natural streams. The length of regulated streams has reached 46,000 km and they are deteriorated ecosystems. Investigations showed that the self-purification of streams from nitrates and phosphates is more effective in natural stretches than in stretches regulated for drainage purposes. Decrease in the average concentration of nitrates in natural and regulated stretches are 8.8 ± 5.0 and 3.0 ± 2.9 mg NO 3 − L−1, respectively. The average coefficient of nitrate self-purification, at a confidence level of 95% in natural stream stretches is 0.50 ± 0.22, and in regulated is −0.15 ± 0.21 km−1, and this difference is essential. The change in the average concentration of phosphates in natural and regulated stretches is almost the same, 0.2 ± 0.1 and 0.2 ± 0.2 mg PO 4 3 − L−1, respectively. The average coefficient of phosphate self-purification, at a confidence level of 95%, in natural stream stretches is 0.28 ± 0.12, in regulated −0.14 ± 0.12 km−1, and this difference is not essential. In terms of the need for the renovation of drainage systems it is suggested that soft naturalization measures are first applied in the streams of Western (Samogitian) Highlands, Coastal Lowlands, and South-Eastern Highlands to improve their self-purification processes.

Mayflies (Ephemeroptera) and Their Contributions to Ecosystem Services

This work is intended as a general and concise overview of Ephemeroptera biology, diversity, and services provided to humans and other parts of our global array of freshwater and terrestrial ecosystems. The Ephemeroptera, or mayflies, are a small but diverse order of amphinotic insects associated with liquid freshwater worldwide. They are nearly cosmopolitan, except for Antarctica and some very remote islands. The existence of the subimago stage is unique among extant insects. Though the winged stages do not have functional mouthparts or digestive systems, the larval, or nymphal, stages have a variety of feeding approaches-including, but not limited to, collector-gatherers, filterers, scrapers, and active predators-with each supported by a diversity of morphological and behavioral adaptations. Mayflies provide direct and indirect services to humans and other parts of both freshwater and terrestrial ecosystems. In terms of cultural services, they have provided inspiration to musicians, poets, and other writers, as well as being the namesakes of various water- and aircraft. They are commemorated by festivals worldwide. Mayflies are especially important to fishing. Mayflies contribute to the provisioning services of ecosystems in that they are utilized as food by human cultures worldwide (having one of the highest protein contents of any edible insect), as laboratory organisms, and as a potential source of antitumor molecules. They provide regulatory services through their cleaning of freshwater. They provide many essential supporting services for ecosystems such as bioturbation, bioirrigation, decomposition, nutrition for many kinds of non-human animals, nutrient cycling and spiraling in freshwaters, nutrient cycling between aquatic and terrestrial systems, habitat for other organisms, and serving as indicators of ecosystem health. About 20% of mayfly species worldwide might have a threatened conservation status due to influences from pollution, invasive alien species, habitat loss and degradation, and climate change. Even mitigation of negative influences has benefits and tradeoffs, as, in several cases, sustainable energy production negatively impacts mayflies.

Taxonomic changes and non-native species: An overview of constraints and new challenges for macroinvertebrate-based indices calculation in river ecosystems

Freshwater ecosystems face many threats in the form of reduced water quantity, poor water quality and the loss of biodiversity. As a result, aquatic biomonitoring tools are required to enable the evaluation of these critical changes. Currently, macroinvertebrate-based indices are globally the most widely used biomonitoring tools in fluvial ecosystems. However, very little is known about the potential effects of changes in taxonomic understanding (updating of classification and nomenclature) or the presence of new non-native species for biotic indices calculation. This is especially relevant given that errors, incorrect classification or exclusion of new/updated nomenclature may affect ecological status evaluations and have direct consequences for the management and conservation of freshwater systems. In this discussion paper the main constraints, challenges and implications of these issues are outlined and case studies from a range of European countries are discussed. However, similar challenges affect rivers and managers globally and will potentially be amplified further in the future. Bioassessment science needs to be open to improvements, and current tools and protocols need to be flexible so that they can be updated and revised rapidly to allow new scientific developments to be integrated. This discussion highlights specific examples and new ideas that may contribute to the future development of aquatic biomonitoring using macroinvertebrates and other faunal and floral groups in riverine ecosystems.

Integrating Meso-Scale Habitat Modelling in the Multicriteria Analysis (MCA) Process for the Assessment of Hydropower Sustainability

The increasing number of water abstractions and water-use conflicts in alpine regions represents a significant threat for these fragile aquatic ecosystems. The use of tools, like multicriteria analysis (MCA), can support related decision-making processes towards sustainable solutions. In this paper, an innovative approach to assess water withdrawals sustainability by integrating the MesoHABSIM (Mesohabitat Simulation Model) into an MCA framework is presented and discussed. The methodology was implemented by replacing, within the MCA assessment, Water Framework Directive biological indicators with the MesoHABSIM based river Habitat Integrity Index, related to watercourse discharge and morphology, which allows quantifying the impacts of withdrawals on river ecosystems and fish communities. The resulting MCA procedure considers four criteria (energy, environment and fishing, landscape, economy) and requires only the use of measurable indicators based on watercourse discharge and its continuous monitoring. It was tested in Aosta Valley region (NW Italy) to both ex ante and ex post scenarios, for different types of water withdrawals and, currently, 20 experimentations, involving 58 hydropower plants and 12 farmer consortia, are ongoing. The proposed MCA process demonstrated its applicability with an increased decision-making quality and involved stakeholders’ satisfaction and is being officially endorsed in the regional River Strategic Plan.

The future of European water management: Demonstration of a new WFD compliant framework to support sustainable management under multiple stress

The Water Framework Directive (WFD), which is the most comprehensive instrument of EU water policy, is more relevant than ever. Sixty percent of Europe's surface water bodies still fail to achieve good ecological status and a multitude of new stressors continue to emerge. A sustained and wholehearted water management effort is therefore of highest priority. Here, we present a new biological assessment approach specifically designed to safeguard sustainable water management under multiple stress. The framework contains three independent elements: 1) an ecological assessment system based on community abundance and composition to quantify ecological status; 2) a diagnostic tool to identify cause(s) of ecological degradation; 3) a management platform to guide the choice of relevant mitigation measures for improvement of the ecological status. The proposed framework is fully compliant with the WFD and currently applied in the assessment of aquatic plant communities in Danish streams. Importantly, the approach presented is not restricted to specific taxonomic groups or ecosystem types but is an example of how a simple approach can bring the conceptual idea of the WFD - that community characteristics in unimpacted, type-specific water bodies should be the backbone in ecological assessments - into practice.

Development and validation of a macroinvertebrate-based biomonitoring tool to assess fine sediment impact in small mountain streams

Increased fine sediment deposition is recognised as one of the major causes of biological impairment of rivers and streams influencing all components of aquatic communities. Notably, stream macroinvertebrates are affected showing changes in abundance and community composition. This makes macroinvertebrates an attractive choice for biomonitoring fine sediment stress. However, there are substantial knowledge gaps regarding the quantification of deposited fine sediment and the identification of taxa sensitive to fine sediment deposition, which could serve as indicators. In this study, we developed a stream type-specific index based on the taxon-specific response of macroinvertebrates to deposited fine sediment in small, coarse substrate-dominated mountain streams. We sampled fine sediment at 73 sampling sites in Western Germany (Europe) in spring 2014 and 2015 using a sediment remobilization technique. Macroinvertebrate taxalists originating from WFD monitoring surveys were available for all sites. We applied Threshold Indicator Taxa ANalysis (TITAN) on the fine sediment mass of the sampling sites and the corresponding macroinvertebrate taxalists to identify indicator taxa, which were then used for index development. In total, TITAN identified 95 reliable indicator taxa, of which some taxa tolerated large amounts of fine sediment (e.g., Gammarus roeselii and Tubificidae Gen. sp.), while others were found to be highly sensitive to increased fine sediment mass (e.g., Elodes sp. and Limnius perrisi). The newly developed index was tested on an independent data set and performed well in detecting fine sediment stress (Spearman's r = 0.63). Furthermore, the index was better related to the deposited fine sediment mass as compared to other fine sediment indices and standard metrics used for monitoring purposes under the Water Framework Directive (WFD). The diagnostic index can be a cost-effective biomonitoring tool for stream managers and can be used as a proxy for the impact of deposited fine sediment on the reach scale.

Environmental correlates of food-chain length, mean trophic level and trophic level variance in invaded riverine fish assemblages

Examining how the trophic structure of biotic assemblages is affected by human impacts, such as habitat degradation and the introduction of alien species, is important for understanding the consequences of such impacts on ecosystem functioning. We used general linear mixed models and hierarchical partitioning analyses of variance to examine for the first time the applicability of three hypotheses (ecosystem-size, productivity and disturbance) for explaining food-chain length (FCL) in invaded fish assemblages. We used Fishbase trophic level (TL) estimates for 16 native and 18 alien fish species in an extensive riverine system in north-eastern Spain (99,700 km², 15 catchments, 530 sites). The FCL of assemblages ranged from 2.7 to 4.42. Ecosystem size-related variables (Strahler stream order, physical habitat diversity) and human-disturbance (conductivity) made the largest contribution to the explained variance in the FCL model after accounting for spatial confounding factors and collinearity among predictors. Within-assemblage TL also was positively associated with Strahler stream order, suggesting that large rivers have the highest trophic diversity. High conductivity was negatively associated with FCL, as did with the mean TL of fish assemblages. However, an inverse association was found between mean TL and Strahler stream order, possibly because the presence of fish species of high TL may be offset by larger numbers of alien species of lower TL in large rivers. Given that there may be trophic replacements among native and alien species, this inference needs to be addressed with detailed trophic studies. However, reducing water conductivity by improved wastewater treatment and better agricultural practices probably would help to conserve the fish species on the apices of aquatic food-webs.

Effects of a glyphosate-based herbicide on Fucus virsoides (Fucales, Ochrophyta) photosynthetic efficiency

Herbicides are increasingly recognised as sources of water pollution. Glyphosate-based herbicides (GBHs) are widely used because of their low cost and high effectiveness. By measuring the photosynthetic efficiency of Fucus virsoides fronds exposed to a GBH (Roundup® Power 2.0), we investigated the effect of a continuous exposure (6 days) and the potential of recovery after a short exposure (24 h). Both experiments were carried out combining GBH with and without nutrient enrichment, simulating a runoff event. A factorial experimental design allowed us to assess the potential of interactions between GBH and nutrients, which are likely to co-occur in coastal areas. Our results show deleterious effects of GBH at low concentration on F. virsoides, independently from the duration of exposure and the presence of nutrients.

Water-quality impacts in semi-arid regions: can natural 'green filters' mitigate adverse effects on fish assemblages?

The effective aridity in riparian areas is increasing from climate change and from human water consumption, which exacerbates the impacts of effluents from wastewater-treatment plants and from catchment run-off in rivers. The potential of natural riparian areas to act as 'green filters' has long been recognized, but the possible ecological benefits of natural riparian areas over large-scale environmental gradients on fish have not been explored in detail. Using an extensive data-set from northeastern Spain (99,700 km², 15 catchments, 530 sites), ours is the first study to ask whether natural riparian vegetation can mitigate the effects of pollution on fish in rivers experiencing water scarcity. We used multimodel inference to explore the additive and interactive effects of riparian vegetation with nutrient pollution and water conductivity, which are among the world's worst river stressors, on multiple fish guilds, including widely distributed species and highly invasive alien fish species. Most models (54%) supported the additive effects of water-quality factors on fish, after having accounted for the influence of geography and hydrological alterations. Although many fewer models (7%) included riparian vegetation as an important predictor, riparian vegetation modulated the forms of the associations between fish and pollution. The relationship of nutrient pollution with native and alien fish richness changed from negative to positive with greater riparian structure or species richness. However, we found the opposite effect for the mean body size of sedentary fish, and only positive additive effects of riparian richness for the probability of occurrence of pelagic fish. Ammonium and nitrite concentrations adversely affected fish in these rivers up to 10 years after the enforcement of the implementation of the Water Framework Directive by the European Union. High conductivity also much affects fish, having negatives associations with migratory, pelagic, invertivorous and native fish, and positive associations with sedentary, benthic, omnivorous and alien fish. Therefore, the current status of natural riparian areas is unlikely to fully mitigate water-quality impacts on fish. The conservation of freshwater resources in semi-arid regions, such as north-eastern Spain, requires improved waste-water treatments and better agriculture practices.

Biological impacts of local vs. regional land use on a small tributary of the Seine River (France): insights from a food web approach based on stable isotopes

As part of the landscape, streams are influenced by land use. Here, we contributed to the understanding of the biological impacts of land use on streams, investigating how landscape effects vary with spatial scales (local vs. regional). We adopted a food web approach integrating both biological structure and functioning, to focus on the overall effect of land use on stream biocœnosis. We selected 17 sites of a small tributary of the Seine River (France) for their contrasted land use, and conducted a natural experiment by sampling three organic matter sources, three macroinvertebrate taxa, and most of the fish community. Using stable isotope analysis, we calculated three food web metrics evaluating two major dimensions of the trophic diversity displayed by the fish community: (i) the diversity of exploited resources and (ii) the trophic level richness. The idea was to examine whether (1) land-use effects varied according to spatial scales, (2) land use affected food webs through an effect on community structure and (3) land use affected food webs through an effect on available resources. Beside an increase in trophic diversity from upstream to downstream, our empirical data showed that food webs were influenced by land use in the riparian corridors (local scale). The effect was complex, and depended on site's position along the upstream-downstream gradient. By contrast, land use in the catchment (regional scale) did not influence stream biocœnosis. At the local scale, community structure was weakly influenced by land use, and thus played a minor role in explaining food web modifications. Our results suggested that the amount of available resources at the base of the food web was partly responsible for food web modifications. In addition, changes in biological functioning (i.e. feeding interactions) can also explain another part of the land-use effect. These results highlight the role played by the riparian corridors as a buffer zone, and advocate that riparian corridor should be at the centre of water management attention.

Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages

Trait-based ecology has been developed for decades to infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive dataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N=389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have ≤3 species (specialization, FSpe; originality, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native:total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive datasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is essential to develop better management strategies.

Predicting New Zealand riverine fish reference assemblages

Biomonitoring is a common method to monitor environmental change in river ecosystems, a key advantage of biomonitoring over snap-shot physicochemical monitoring is that it provides a more stable, long-term insight into change that is also effects-based. In New Zealand, the main biomonitoring method is a macroinvertebrate sensitivity scoring index, with little established methods available for biomonitoring of fish. This study models the contemporary distribution of common freshwater fish and then uses those models to predict freshwater fish assemblages for each river reach under reference conditions. Comparison of current fish assemblages with those predicted in reference conditions (as observed/expected (O/E) ratios) may provide a suitable option for freshwater fish biomonitoring. Most of the fish communities throughout the central North Island and lower reaches show substantial deviation from the modelled reference community. Most of this deviation is explained by nutrient enrichment, followed by downstream barriers (i.e. dams) and loss of riparian vegetation. The presence of modelled introduced species had relatively little impact on the presence of the modelled native fish. The maps of O/E fish assemblage may provide a rapid way to identify potential restoration sites.

Disentangling the effects of low pH and metal mixture toxicity on macroinvertebrate diversity

One of the primary goals of biological assessment of streams is to identify which of a suite of chemical stressors is limiting their ecological potential. Elevated metal concentrations in streams are often associated with low pH, yet the effects of these two potentially limiting factors of freshwater biodiversity are rarely considered to interact beyond the effects of pH on metal speciation. Using a dataset from two continents, a biogeochemical model of the toxicity of metal mixtures (Al, Cd, Cu, Pb, Zn) and quantile regression, we addressed the relative importance of both pH and metals as limiting factors for macroinvertebrate communities. Current environmental quality standards for metals proved to be protective of stream macroinvertebrate communities and were used as a starting point to assess metal mixture toxicity. A model of metal mixture toxicity accounting for metal interactions was a better predictor of macroinvertebrate responses than a model considering individual metal toxicity. We showed that the direct limiting effect of pH on richness was of the same magnitude as that of chronic metal toxicity, independent of its influence on the availability and toxicity of metals. By accounting for the direct effect of pH on macroinvertebrate communities, we were able to determine that acidic streams supported less diverse communities than neutral streams even when metals were below no-effect thresholds. Through a multivariate quantile model, we untangled the limiting effect of both pH and metals and predicted the maximum diversity that could be expected at other sites as a function of these variables. This model can be used to identify which of the two stressors is more limiting to the ecological potential of running waters.