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DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Defining nutrient thresholds that protect and support the ecological integrity of aquatic ecosystems is a fundamental step in maintaining their natural biodiversity and preserving their resilience. With increasing catchment pressures and climate change, it is more important than ever to develop clear methods to establish thresholds for status classification and management of waters. This must often be achieved using complex data and should be robust to interference from additional pressures as well as ameliorating or confounding conditions. We use both artificial and real data to examine challenges in setting nutrient thresholds in unbalanced and skewed data. We found significant advantages to using binary logistic regression over other techniques. However, one of the key challenges is objectively selecting a probability from which to derive the nutrient threshold. For this purpose, the examination of the proportions of matching and mismatching status classifications of nutrients and a biological quality element using a confusion matrix is a key step that should be more widely adopted in threshold selection. We examined a large array of statistical measures of classification accuracy and their performance over combinations of skewness and imbalance in the data. The most appropriate threshold probability is a compromise between maximising overall classification accuracy and reducing mismatches expressed as commission (false positives) without excessive omission (false negatives). An application to a lake type indicated total phosphorus thresholds that would be around 50 μg l -1 lower than the threshold achieved by an 'unguided' approach, indicating that this approach is a very significant development meriting attention from national authorities responsible for water management., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Anthropogenic climate change and landscape alteration are two of the most important threats to the terrestrial and aquatic ecosystems of the tropical Americas, thus jeopardizing water and soil resources for millions of people in the Andean nations. Understanding how aquatic ecosystems will respond to anthropogenic stressors and accelerated warming requires shifting from short-term and static to long-term, dynamic characterizations of human-terrestrial-aquatic relationships. Here we use sediment records from Lake Llaviucu, a tropical mountain Andean lake long accessed by Indigenous and post-European societies, and hypothesize that under natural historical conditions (i.e., low human pressure) vegetation and aquatic ecosystems' responses to change are coupled through indirect climate influences-that is, past climate-driven vegetation changes dictated limnological trajectories. We used a multi-proxy paleoecological approach including drivers of terrestrial vegetation change (pollen), soil erosion (Titanium), human activity (agropastoralism indicators), and aquatic responses (diatoms) to estimate assemblage-wide rates of change and model their synchronous and asynchronous (lagged) relationships using Generalized Additive Models. Assemblage-wide rate of change results showed that between ca. 3000 and 400 calibrated years before present (cal years BP) terrestrial vegetation, agropastoralism and diatoms fluctuated along their mean regimes of rate of change without consistent periods of synchronous rapid change. In contrast, positive lagged relationships (i.e., asynchrony) between climate-driven terrestrial pollen changes and diatom responses (i.e., asynchrony) were in operation until ca. 750 cal years BP. Thereafter, positive lagged relationships between agropastoralism and diatom rates of changes dictated the lake trajectory, reflecting the primary control of human practices over the aquatic ecosystem prior European occupation. We interpret that shifts in Indigenous practices (e.g., valley terracing) curtailed nutrient inputs into the lake decoupling the links between climate-driven vegetation changes and the aquatic community. Our results demonstrate how rates of change of anthropogenic and climatic influences can guide dynamic ecological baselines for managing water ecosystem services in the Andes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

One key component of any eutrophication management strategy is establishment of realistic thresholds above which negative impacts become significant and provision of ecosystem services is threatened. This paper introduces a toolkit of statistical approaches with which such thresholds can be set, explaining their rationale and situations under which each is effective. All methods assume a causal relationship between nutrients and biota, but we also recognise that nutrients rarely act in isolation. Many of the simpler methods have limited applicability when other stressors are present. Where relationships between nutrients and biota are strong, regression is recommended. Regression relationships can be extended to include additional stressors or variables responsible for variation between water bodies. However, when the relationship between nutrients and biota is weaker, categorical approaches are recommended. Of these, binomial regression and an approach based on classification mismatch are most effective although both will underestimate threshold concentrations if a second stressor is present. Whilst approaches such as changepoint analysis are not particularly useful for meeting the specific needs of EU legislation, other multivariate approaches (e.g. decision trees) may have a role to play. When other stressors are present quantile regression allows thresholds to be established which set limits above which nutrients are likely to influence the biota, irrespective of other pressures. The statistical methods in the toolkit may be useful as part of a management strategy, but more sophisticated approaches, often generating thresholds appropriate to individual water bodies rather than to broadly defined "types", are likely to be necessary too. The importance of understanding underlying ecological processes as well as correct selection and application of methods is emphasised, along with the need to consider local regulatory and decision-making systems, and the ease with which outcomes can be communicated to non-technical audiences., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The European Union has embarked on a policy which aims to achieve good ecological status in all surface waters (i.e. rivers, lakes, transitional and coastal waters). In theory, ecological status assessment methods should address the effects of all relevant human pressures. In this study, we analyze the degree to which methods European countries use to assess ecological status tackle various pressures affecting European waters. Nutrient pollution is by far the best-covered pressure for all four water categories. Out of total of 423 assessment methods, 370 assess eutrophication and pressure-specific relationships have been demonstrated for 212 of these. "General degradation" is addressed by 238 methods, mostly validated by relationships to combined pressure indices. Other major pressures have received significantly less effort: hydromorphological degradation is assessed by 160 methods and pressure-specific relationships have been demonstrated for just 40 of these. Hydromorphological pressures are addressed (at least by one BQE) only by 25% countries for coastal waters and 70-80% for lakes and transitional waters. Specific diagnostic tools (i.e. single-pressure relationships) for hydromorphology have only been developed by a few countries: only 20% countries have such methods for lakes, coastal and transitional waters and less than half for rivers. Toxic contamination is addressed by 90 methods; however, pressure-specific relationships have been demonstrated for just eight of these. Only two countries have demonstrated pressure-specific acidification methods for rivers, and three for lakes. In summary, methods currently in use mostly address eutrophication and/or general degradation, but there is not much evidence that they reliably pick up the effects of other significant pressures such as hydromorphology or toxic contamination. Therefore, we recommend that countries re-examine: (1) those pressures which affect different water categories in the country; (2) relevant assessment methods to tackle those pressures; (3) whether pressure-response relationships have been developed for each of these., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

There is growing evidence that river temperatures are increasing under climate change, which is expected to be exacerbated by increased abstractions to satisfy human water demands. Water temperature research has experienced crucial advances, both in terms of developing new monitoring and modelling tools, as well as understanding the mechanisms of temperature feedbacks with biogeochemical and ecological processes. However, water practitioners and regulators are challenged with translating the widespread and complex technological, modelling and conceptual advances made in river temperature research into improvements in management practice. This critical review provides a comprehensive overview of recent advances in the state-of-the-art monitoring and modelling tools available to inform ecological research and practice. In so doing, we identify pressing research gaps and suggest paths forward to address practical research and management challenges. The proposed research directions aim to provide new insights into spatio-temporal stream temperature dynamics and unravel drivers and controls of thermal river regimes, including the impacts of changing temperature on metabolism and aquatic biogeochemistry, as well as aquatic organisms. The findings of this review inform future research into ecosystem resilience in the face of thermal degradation and support the development of new management strategies cutting across spatial and temporal scales., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)