The biological condition gradient: a descriptive model for interpreting change in aquatic ecosystems

Towards harmonized standards for freshwater biodiversity monitoring and biological assessment using benthic macroinvertebrates

Monitoring programs at sub-national and national scales lack coordination, harmonization, and systematic review and analysis at continental and global scales, and thus fail to adequately assess and evaluate drivers of biodiversity and ecosystem degradation and loss at large spatial scales. Here we review the state of the art, gaps and challenges in the freshwater assessment programs for both the biological condition (bioassessment) and biodiversity monitoring of freshwater ecosystems using the benthic macroinvertebrate community. To assess the existence of nationally- and regionally- (sub-nationally-) accepted freshwater benthic macroinvertebrate protocols that are put in practice/used in each country, we conducted a survey from November 2022 to May 2023. Responses from 110 respondents based in 67 countries were received. Although the responses varied in their consistency, the responses clearly demonstrated a lack of biodiversity monitoring being done at both national and sub-national levels for lakes, rivers and artificial waterbodies. Programs for bioassessment were more widespread, and in some cases even harmonized among several countries. We identified 20 gaps and challenges, which we classed into five major categories, these being (a) field sampling, (b) sample processing and identification, (c) metrics and indices, (d) assessment, and (e) other gaps and challenges. Above all, we identify the lack of harmonization as one of the most important gaps, hindering efficient collaboration and communication. We identify the IUCN SSC Global Freshwater Macroinvertebrate Sampling Protocols Task Force (GLOSAM) as a means to address the lack of globally-harmonized biodiversity monitoring and biological assessment protocols.

Fuzzy logic as a novel approach to predict biological condition gradient of various streams in Ceyhan River Basin (Turkey)

Creating a method to categorize the ecological status of streams according to their biological conditions and establishing scientifically defensible nutrient criteria to protect their biotic integrity poses significant challenges. Biomonitoring of least disturbed areas is an important issue to accurately assess the ecological status of surface waters and ensure their sustainability. The fuzzy logic as a novel approach was firstly applied to evaluate the biological condition gradient of 44 sampled streams in the Ceyhan River Basin, utilizing two diatom indices, total phosphorus (TP), electrical conductivity (EC), and CORINE data. The fuzzy logic was employed to examine variations in the diatom compositions and land cover based on biological condition gradients (BCGs) of various streams and to assess the suitability of BCG in evaluating the health of studied stream systems. A three-layer fuzzy logic was constructed to predict BCGs of steams based on input data, with diatom metrics, TP, and EC representing BCGdia and land cover variables contributing to BCGland. The effects of operating variables were studied to optimize BCG results. The highest BCG score (0.85) was determined in Aksu Spring Brook in the spring, whereas the lowest value (0.05) was calculated in Erkenez Stream3 in the summer. BCGs showed strong relationships with nutrients, altitude, and EC. Results of BCGs indicated that sampling stations have various ecological statuses ranging from bad to high in the Ceyhan River Basin. The BCGdia and BCGland made important contributions to determine the ecological status of streams in the Ceyhan River Basin. Results showed that the BCG approach allows a more reliable way to determine the ecological status of streams in the Ceyhan River Basin by combining biological and chemical assessments for the sustainability of the environment. It is recommended that the BCG will be applied and evaluated in future research studies across various river basins, both within and outside of Turkey.

Development of a macroinvertebrate-based biotic index to assess water quality of rivers in Niger State, North Central Ecoregion of Nigeria

The increasing pollution of lotic ecosystems in sub-Saharan Africa, particularly in Nigeria, poses a threat to water quality, public health and biodiversity. It is therefore essential to develop appropriate tools and methods for monitoring these rivers, particularly in heavily affected areas, where these water resources are vital to the surrounding communities that are heavily dependent on them. To fill this gap, we propose to develop a multimetric index based on macroinvertebrates for the assessment of ecological quality of rivers in Niger State (NSRBI). Eighty-eight metrics were evaluated through a step-by-step statistical process (namely, range test and stability, redundancy test and relationship with abiotic variables), in which metrics that did not meet the conditions were excluded. At the end of this process, only four metrics (%Hemiptera, Diptera richness, Pielou equitability and % of very large individuals (size > 40 mm)) fulfilling all criteria were included in the index. These metrics were then scored on a continuous scale and divided into four water quality classes: "very poor", "poor", "fair" and "good". Evaluation of the performance of the index on test sites showed a correspondence of 90% between index result and environmental-based classification. Therefore, the NSRBI could be a valuable tool for monitoring and assessing the ecological conditions of rivers in Niger State and the North Central Nigeria ecoregion predominantly in urban and agricultural landscapes.

Striving for consistent bioassessment across diverse landscapes: Using land use matters for classifying reference and disturbed sites for index development

Consistency in ecological assessments is challenging across large diverse landscapes because natural geological, climatic, and hydrological factors vary greatly. As a result, large landscapes are often subdivided into ecoregions and assessments are based on ecoregion specific indices. In the present study, we developed and compared multimetric indices (MMIs) using benthic diatom data from the 2008-2009 dataset from the United States (US) National Rivers and Streams Assessment. Nationwide and separate ecoregion specific MMIs were developed with reference, moderately disturbed, and highly disturbed sites selected using criteria based on physicochemical condition of the habitat or based on watershed land use (% agriculture and % urban). Metrics were adjusted to account for variation in natural conditions when needed. We found only land use criteria selected reference sites with consistently low median % watershed disturbance (%WD) and large differences in %WD between reference and highly disturbed sites. <38 % of sites were identified as reference or highly disturbed by both physicochemical and land use criteria. All MMIs displayed substantial discrimination ability between reference and highly disturbed sites. At the national scale, MMIs based on land use outperformed MMIs based on physicochemical conditions for all performance attributes tested. When national scale MMIs were applied to ecoregions, MMIs based on land use were again better than MMIs based on physicochemical conditions for most performance attributes and even had better or comparable performance to the land use MMIs developed separately for each ecoregion. Our findings show that developing MMIs using land use criteria and adjusting metrics for natural variation could improve assessment consistency without losing MMI performance across large, diverse landscapes as in the US National Rivers and Streams Assessment.

The distribution of diatom assemblages with the effects of environmental parameters and ecological status assessment based on diatom indices in the lentic systems of the Akarçay and Asi Basins (Türkiye)

In order to detect the effects of different stressors on the littoral diatom assemblages and biodiversity of the lentic systems in two different basins in Türkiye, 15 lentic systems in the Akarçay and Asi basins were sampled three times (spring, summer, and fall) for littoral diatoms and environmental variables. The biological assessment of these sites was also evaluated using 9 different river and lake diatom indices. Based on the total phosphorus (TP), total nitrogen (TN), electrical conductivity (EC), salinity (SAL) values, and dominant diatom species, three lentic systems in Akarçay Basin (Lake Eber, 26 Ağustos Pond, and Lake Karamık) were more eutrophic and under the pressure of anthropogenic and climatic (precipitation) stressors. Trophic diatom index for lakes (TDIL) showed a higher correlation with TN and TP and was the most effective index in explaining ecological quality in 15 lentic systems. The species richness of diatoms was also negatively affected by EC and SAL values. The lentic systems of the two basins were separated from each other based on the species composition and the distribution of the dominant species with the effect of altitude (ALT). Considering the distribution of diatom assemblage of the lentic systems in these two basins, anthropogenic, climatic, and geographical factors have become prominent to shape the diatom community structure.

Patterns in and predictors of stream and river macroinvertebrate genera and fish species richness across the conterminous USA

Both native and non-native taxa richness patterns are useful for evaluating areas of greatest conservation concern. To determine those patterns, we analyzed fish and macroinvertebrate taxa richness data obtained at 3475 sites collected by the USEPA's National Rivers and Streams Assessment. We also determined which natural and anthropogenic variables best explained patterns in regional richness. Macroinvertebrate and fish richness increased with the number of sites sampled per region. Therefore, we determined residual taxa richness from the deviation of observed richness from predicted richness given the number of sites per region. Regional richness markedly exceeded average site richness for both macroinvertebrates and fish. Predictors of macroinvertebrate-genus and fish-species residual-regional richness differed. Air temperature was an important predictor in both cases but was positive for fish and negative for macroinvertebrates. Both natural and land use variables were significant predictors of regional richness. This study is the first to determine mean site and regional richness of both fish and aquatic macroinvertebrates across the conterminous USA, and the key anthropogenic drivers of regional richness. Thus, it offers important insights into regional USA biodiversity hotspots.

Observed and projected functional reorganization of riverine fish assemblages from global change

Climate and land-use/land-cover change ("global change") are restructuring biodiversity, globally. Broadly, environmental conditions are expected to become warmer, potentially drier (particularly in arid regions), and more anthropogenically developed in the future, with spatiotemporally complex effects on ecological communities. We used functional traits to inform Chesapeake Bay Watershed fish responses to future climate and land-use scenarios (2030, 2060, and 2090). We modeled the future habitat suitability of focal species representative of key trait axes (substrate, flow, temperature, reproduction, and trophic) and used functional and phylogenetic metrics to assess variable assemblage responses across physiographic regions and habitat sizes (headwaters through large rivers). Our focal species analysis projected future habitat suitability gains for carnivorous species with preferences for warm water, pool habitats, and fine or vegetated substrates. At the assemblage level, models projected decreasing habitat suitability for cold-water, rheophilic, and lithophilic individuals but increasing suitability for carnivores in the future across all regions. Projected responses of functional and phylogenetic diversity and redundancy differed among regions. Lowland regions were projected to become less functionally and phylogenetically diverse and more redundant while upland regions (and smaller habitat sizes) were projected to become more diverse and less redundant. Next, we assessed how these model-projected assemblage changes 2005-2030 related to observed time-series trends (1999-2016). Halfway through the initial projecting period (2005-2030), we found observed trends broadly followed modeled patterns of increasing proportions of carnivorous and lithophilic individuals in lowland regions but showed opposing patterns for functional and phylogenetic metrics. Leveraging observed and predicted analyses simultaneously helps elucidate the instances and causes of discrepancies between model predictions and ongoing observed changes. Collectively, results highlight the complexity of global change impacts across broad landscapes that likely relate to differences in assemblages' intrinsic sensitivities and external exposure to stressors.

Mountaintop removal coal mining impacts on structural and functional indicators in Central Appalachian streams

Mountaintop removal coal mining (MTR) has been a major source of landscape change in the Central Appalachians of the United States (US). Changes in stream hydrology, channel geomorphology and water quality caused by MTR coal mining can lead to severe impairment of stream ecological integrity. The objective of the Clean Water Act (CWA) is to restore and maintain the ecological integrity of the Nation's waters. Sensitive, readily measured indicators of ecosystem structure and function are needed for the assessment of stream ecological integrity. Most CWA assessments rely on structural indicators; inclusion of functional indicators could make these assessments more holistic and effective. The goals of this study were: (1) test the efficacy of selected carbon (C) and nitrogen (N) cycling and microbial structural and functional indicators for assessing MTR coal mining impacts on streams; (2) determine whether indicators respond to impacts in a predictable manner; and (3) determine if functional indicators are less likely to change than are structural indicators in response to stressors associated with MTR coal mining. The structural indicators are water quality and sediment organic matter concentrations, and the functional indicators relate to microbial activity and biofilm production. Seasonal measurements were conducted over the course of a year in streams draining small MTR-impacted and forested watersheds in the Twentymile Creek watershed of West Virginia (WV). Five of the eight structural parameters measured had significant responses, with all means greater in the MTR-impacted streams than in the forested streams. These responses resulted from changes in source or augmentation of the original source of the C and N structural parameters because of MTR coal mining. Nitrate concentration and the stable carbon isotopic ratio of dissolved inorganic carbon were the most effective indicators evaluated in this study. Only three of the fourteen functional indicators measured had significant responses to MTR coal mining, with all means greater in the forested streams than in the MTR-impacted streams. These results suggest that stressors associated with MTR coal mining caused reduction in some aspects of microbial cycling, but resource subsidies may have counterbalanced some of the inhibition leading to no observable change in most of the functional indicators. The detritus base, which is thought to confer functional stability, was likely sustained in the MTR-impacted streams by channel storage and/or leaf litter inputs from their largely intact riparian zones. Overall, our results largely support the hypothesis that certain functional processes are more resistant to stress induced change than structural properties but also suggest the difficulty of identifying suitable functional indicators for ecological integrity assessment.

The gap between experts, farmers and non-farmers on perceived environmental vulnerability and the influence of values and beliefs

Science has played a mixed role in guiding conservation and sustainability-oriented decision-making by individuals, policymakers, institutions, and governments. Not all science-based conservation and sustainability initiatives that address issues facing humanity and ecosystems and global problems have gained public support. Conservation decisions and policy prescriptions are and may be based on perceptions about and experiences with the environment, local land use, and ecosystems that may not align with or be grounded in science or evidence from experts in the field. Values, beliefs, and perceptions associated with nature play a critical role in how individuals view biodiversity conservation, sustainability, and natural resource management. This study first examines the gap between experts (scientists and other field experts) and the public (farmers and non-farmers) about the state of water and land resources, wildlife and associated habitats, and aquatic biodiversity in the Smoky Hill River Watershed in western Kansas. Second, the study examines the role that values and beliefs play in shaping environmental perceptions for farmers and non-farmers. Analysis confirms that a gap between experts and farmers/non-farmers does exist, especially with respect to the state of the Ogallala Aquifer, playas, rivers and streams, lakes and reservoirs, native grasslands, wildlife habitats, farmland, native fish populations, and wildlife species. Ordered-logistic regression analyses, meanwhile, indicate that farmer and non-farmer perceptions about the state of the local environment are influenced by traditional and self-interested values, as well as environmental values and beliefs, but less so by religiosity and political ideology. Despite broad takeaways, results exhibited heterogeneity across the farmer and non-farmer subpopulations. If environmental professionals cannot align ecological data, stakeholders' values/perceptions, and policies, then the existing body of technical research and management on sustainability in natural and social sciences may be of little value.

A biological condition gradient for coral reefs in the US Caribbean Territories: Part I. Coral narrative rules

As coral reef condition and sustainability continue to decline worldwide, losses of critical habitat and their ecosystem services have generated an urgency to understand and communicate reef response to management actions, environmental contamination, and natural disasters. Increasingly, coral reef protection and restoration programs emphasize the need for robust assessment tools for protecting high-quality waters and establishing conservation goals. Of equal importance is the need to communicate assessment results to stakeholders, beneficiaries, and the public so that environmental consequences of decisions are understood. The Biological Condition (BCG) model provides a structure to evaluate the condition of a coral reef in increments of change along a gradient of human disturbance. Communication of incremental change, regardless of direction, is important for decision makers and the public to better understand what is gained or lost depending on what actions are taken. We developed a narrative (qualitative) Biological Condition Gradient (BCG) from the consensus of a diverse expert panel to provide a framework for coral reefs in US Caribbean Territories. The model uses narrative descriptions of biological attributes for benthic organisms to evaluate reefs relative to undisturbed or minimally disturbed conditions. Using expert elicitation, narrative decision rules were proposed and deliberated to discriminate among six levels of change along a gradient of increasing anthropogenic stress. Narrative rules for each of the BCG levels are presented to facilitate the evaluation of benthic communities in coral reefs and provide specific narrative features to detect changes in coral reef condition and biological integrity. The BCG model can be used in the absence of numeric, or quantitative metrics, to evaluate actions that may encroach on coral reef ecosystems, manage endangered species habitat, and develop and implement management plans for marine protected areas, watersheds, and coastal zones. The narrative BCG model is a defensible model and communication tool that translates scientific results so the nontechnical person can understand and support both regulatory and non-regulatory water quality and natural resource programs.

Establishing ecologically-relevant nutrient thresholds: A tool-kit with guidance on its use

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.

A biological condition gradient for Caribbean coral reefs: Part II. Numeric rules using sessile benthic organisms

The Biological Condition Gradient (BCG) is a conceptual model used to describe incremental changes in biological condition along a gradient of increasing anthropogenic stress. As coral reefs collapse globally, scientists and managers are focused on how to sustain the crucial structure and functions, and the benefits that healthy coral reef ecosystems provide for many economies and societies. We developed a numeric (quantitative) BGC model for the coral reefs of Puerto Rico and the US Virgin Islands to transparently facilitate ecologically meaningful management decisions regarding these fragile resources. Here, reef conditions range from natural, undisturbed conditions to severely altered or degraded conditions. Numeric decision rules were developed by an expert panel for scleractinian corals and other benthic assemblages using multiple attributes to apply in shallow-water tropical fore reefs with depths <30 m. The numeric model employed decision rules based on metrics (e.g., % live coral cover, coral species richness, pollution-sensitive coral species, unproductive and sediment substrates, % cover by Orbicella spp.) used to assess coral reef condition. Model confirmation showed the numeric BCG model predicted the panel's median site ratings for 84% of the sites used to calibrate the model and 89% of independent validation sites. The numeric BCG model is suitable for adaptive management applications and supports bioassessment and criteria development. It is a robust assessment tool that could be used to establish ecosystem condition that would aid resource managers in evaluating and communicating current or changing conditions, protect water and habitat quality in areas of high biological integrity, or develop restoration goals with stakeholders and other public beneficiaries.

Biological assessment of western USA sandy bottom rivers based on modeling historical and current fish and macroinvertebrate data

Biological monitoring is important for assessing the ecological condition of surface waters. However, there are challenges in determining what constitutes reference conditions, what assemblages should be used as indicators, and how assemblage data should be converted into quantitative indicator scores. In this study, we developed and applied biological condition gradient (BCG) modeling to fish and macroinvertebrate data previously collected from large, sandy bottom southwestern USA rivers. Such rivers are particularly vulnerable to altered flow regimes resulting from dams, water withdrawals and climate change. We found that sensitive ubiquitous taxa for both fish and macroinvertebrates had been replaced by more tolerant taxa, but that the condition assessment ratings based on fish and macroinvertebrate assemblages differed. We conclude that the BCG models based on both macroinvertebrate and fish assemblage condition were useful for classifying the condition of southwestern USA sandy bottom rivers. However, our fish BCG model was slightly more sensitive than the macroinvertebrate model to anthropogenic disturbance, presumably because we had historical fish data, and because fish may be more sensitive to dams and altered flow regimes than are macroinvertebrates.

Evaluating the impact of watershed development and climate change on stream ecosystems: A Bayesian network modeling approach

A continuous-variable Bayesian network (cBN) model is used to link watershed development and climate change to stream ecosystem indicators. A graphical model, reflecting our understanding of the connections between climate change, weather condition, loss of natural land cover, stream flow characteristics, and stream ecosystem indicators is used as the basis for selecting flow metrics for predicting macroinvertebrate-based indicators. Selected flow metrics were then linked to variables representing watershed development and climate change. We fit the model to data from two river basins in southeast US and the resulting model was used to simulate future stream ecological conditions using projected future climate and development scenarios. The three climate models predicted varying ecological condition trajectories, but similar worst-case ecological conditions. The established modeling approach couples mechanistic understanding with field data to develop predictions of management-relevant variables across a heterogeneous landscape. We discussed the transferability of the modeling approach.

Time marches on, but do the causal pathways driving instream habitat and biology remain consistent?

Stream ecosystems are complex networks of interacting terrestrial and aquatic drivers. To untangle these ecological networks, efforts evaluating the direct and indirect effects of landscape, climate, and instream predictors on biological condition through time are needed. We used structural equation modeling and leveraged a stream survey program to identify and compare important predictors driving condition of benthic macroinvertebrate and fish assemblages. We used data resampled 14 years apart at 252 locations across Maryland, USA. Sample locations covered a wide range of conditions that varied spatiotemporally. Overall, the relationship directions were consistent between sample periods, but their relative strength varied temporally. For benthic macroinvertebrates, we found that the total effect of natural landscape (e.g., elevation, longitude, latitude, geology) and land use (i.e., forest, development, agriculture) predictors was 1.4 and 1.5 times greater in the late 2010s compared to the 2000s. Moreover, the total effect of water quality (e.g., total nitrogen and conductivity) and habitat (e.g., embeddedness, riffle quality) was 1.2 and 4.8 times lower in the 2010s, respectively. For fish assemblage condition, the total effect of land use-land cover predictors was 2.3 times greater in the 2010s compared to the 2000s, while the total effect of local habitat was 1.4 times lower in the 2010s, respectively. As expected, we found biological assemblages in catchments with more agriculture and urban development were generally comprised of tolerant, generalist species, while assemblages in catchments with greater forest cover had more-specialized, less-tolerant species (e.g., Ephemeroptera, Plecoptera, and Trichoptera taxa, clingers, benthic and lithophilic spawning fishes). Changes in the relative importance of landscape and land-use predictors suggest other correlated, yet unmeasured, proximal factors became more important over time. By untangling these ecological networks, stakeholders can gain a better understanding of the spatiotemporal relationships driving biological condition to implement management practices aimed at improving stream condition.

Agricultural Effects on Streams and Rivers: A Western USA Focus

Globally, croplands and rangelands are major land uses and they have altered lands and waters for millennia. This continues to be the case throughout the USA, despite substantial improvements in treating wastewaters from point sources—versus non-point (diffuse) sources. Poor macroinvertebrate assemblage condition occurs in 30% of conterminous USA streams and rivers; poor fish assemblage condition occurs in 26%. The risk of poor fish assemblage condition was most strongly associated with excess nutrients, salinity and sedimentation and impaired riparian woody vegetation. Although the Clean Water Act was passed to restore and maintain the integrity of USA waters, that will be impossible without controlling agricultural pollution. Likewise, the Federal Land Policy and Management Act was enacted to protect the natural condition of public lands and waters, including fish habitat, but it has failed to curtail the sacred cows of livestock grazing. Although progress has been slow and spotty, promising results have been obtained from basin and watershed planning and riparian zone protections.

Improving biological condition assessment accuracy by multimetric index approach with microalgae in streams and lakes

Multimetric index (MMI) approach is a broadly used in ecological assessment because it can integrate information of various kinds of ecologically related metrics of freshwater ecosystems and provide an easily understandable score for purpose of further evaluation and managements. Accounting for natural variation and disentangling covariation between natural environmental factors and human disturbance factors are imperative for an accurate assessment. Lots of progress has been made recently on the aforementioned two aspects. Three approaches, a priori classification of sites by regions or typologies, site-specific modeling of expected reference condition and varying metrics in site groups, have been tested in lakes and streams to improve assessment accuracy. All existed studies support that site-specific modeling can efficiently account for natural variation and generate a MMI with good performance. However, until now, no strong evidence has shown that diatom/blue-algae typologies are better than regionalization frameworks on accounting for natural variation either in lakes or in streams. To separate the natural variation explained by site specific modeling from that of varying metrics is necessary for a thorough and accurate evaluation on the valuableness of site-grouping by typologies. Different performance of varying metrics among site groups of streams and lakes was most probably caused by the lack of representativeness of diatom metrics on biological condition rather than the complex multi-stressor gradients in streams and rivers. A recent study showed that blue-green algae enhanced performance of diatom-based MMI on defining lake condition under high level of human disturbance. On the other hand, with more and more extensive and intensive use of statistics techniques in developing MMI, we also discussed some statistical challenges faced by scientists in field of ecological assessment, especially on setting significance level of a statistical test and multiple comparison issue in MMI performance comparison.

Effects of thorium on bacterial, microalgal and micromeiofaunal community structures in a periphytic biofilm

Few ecotoxicity studies are available on thorium (Th) which hinders the ability to evaluate its ecotoxicological risk. Its release in the environment is often associated with the extraction of rare earth elements and uranium, as well as the field applications of phosphate fertilizers. This study investigates the effects of Th on microbial communities of periphytic biofilms. Ceramic plates were left to colonize for one month in the laboratory with a biofilm sampled from Cap Rouge river (QC, Canada). Plates were randomly placed in channels containing culture media representing three different conditions: a control condition (C0; background Th concentrations of 0.004 ± 0.002 nM), a low Th concentration condition (C1; 0.18 ± 0.09 nM Th) and a moderately high Th condition (C10; 8.7 ± 3.4 nM) for up to 4 weeks. The presence of Th modified the diatom community by changing its taxonomic structure, reducing diversity and increasing cell density. The taxonomic structure of the bacterial community, followed by 16S metabarcoding analysis, was affected with a significant decrease in Pseudanabaena and Shingopyxis genera in the two Th exposed conditions. No direct toxic effect of Th was observed on counted micromeiofauna but the changes in diatom and bacterial communities could explain the higher number of individual diatoms and micromeiofauna observed in Th-exposed conditions. This work shows that low concentrations of Th can modify biofilm structure, which, in turn, could disturb its ecologically key functions.

Setting the Phosphorus Boundaries for Greek Natural Shallow and Deep Lakes for Water Framework Directive Compliance

Eutrophication caused by nutrient enrichment is a predominant stressor leading to lake degradation and, thus, the set-up of boundaries that support good ecological status, the Water Framework Directive’s main target, is a necessity. Greece is one of the Member States that have recorded delays in complying with the coherent management goals of European legislation. A wide range of different statistical approaches has been proposed in the Best Practice Guide for determining appropriate nutrient thresholds. To determine the nutrient thresholds supporting the good status of natural Greek lakes, the phytoplankton dataset gathered from the national monitoring programme (2015–2020) was used for shallow and deep natural lakes. The regression analyses were sufficient and robust in order to derive total phosphorus thresholds that ranged from 20 to 41 μg/L in shallow and 15–32 μg/L in deep natural lake types. Nutrient boundaries that encompass the stressors these lakes are subject to, are essential in proper lake management design.

Correspondence between a recreational fishery index and ecological condition for U.S.A. streams and rivers

Sport fishing is an important recreational and economic activity, especially in Australia, Europe and North America, and the condition of sport fish populations is a key ecological indicator of water body condition for millions of anglers and the public. Despite its importance as an ecological indicator representing the status of sport fish populations, an index for measuring this ecosystem service has not been quantified by analyzing actual fish taxa, size and abundance data across the U.S.A. Therefore, we used game fish data collected from 1,561 stream and river sites located throughout the conterminous U.S.A. combined with specific fish species and size dollar weights to calculate site-specific recreational fishery index (RFI) scores. We then regressed those scores against 38 potential site-specific environmental predictor variables, as well as site-specific fish assemblage condition (multimetric index; MMI) scores based on entire fish assemblages, to determine the factors most associated with the RFI scores. We found weak correlations between RFI and MMI scores and weak to moderate correlations with environmental variables, which varied in importance with each of 9 ecoregions. We conclude that the RFI is a useful indicator of a stream ecosystem service, which should be of greater interest to the USA public and traditional fishery management agencies than are MMIs, which tend to be more useful for ecologists, environmentalists and environmental quality agencies.

Identification of Priority Conservation Areas for Protected Rivers Based on Ecosystem Integrity and Authenticity: A Case Study of the Qingzhu River, Southwest China

The establishment of protected areas for a river (PARs) is an efficient approach for the conservation of its ecosystem and biodiversity. This study selected the free-flowing Qingzhu River, located in the mountains of southwest China and one of 34 global biodiversity hotspots, as a case study. This study applied the ecosystem approach to develop a model for identifying priority conservation areas for a river (PCARs) based on integrity and authenticity. Three model elements were selected, namely streams, forest and human activity, characterized by three indicators: irreplaceability, tree cover and human activity, respectively. The spatial distributions of these indicators were overlaid according to different weights to generate a map (SCPV) of comprehensive protected value (CPV), which was used to indicate ecosystem integrity and authenticity in the study catchment. Lastly, PCARs were identified by comparing existing protected areas with the calculated SCPV. The application of the model to the Qingzhu River indicated the area of PCARs to be ~71.88 km2, accounting for 15.13% of the total PAR area. Priority reaches for protection were then identified, with many falling within the mainstem of the river in the middle and lower reaches. The total length of priority protected reaches was ~75.97 km, accounting for 49.33% of the total length of the river mainstem within Qingchuan County. This study validated the model at both the theoretical and practical level, confirming that the model is useful for facilitating the precise protection and smart management of rivers.

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms as well as macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes that currently only use the kick-net technique to sample macroinvertebrates.

Development of a reef fish biological condition gradient model with quantitative decision rules for the protection and restoration of coral reef ecosystems

Coral reef ecosystems are declining due to multiple interacting stressors. A bioassessment framework focused on stressor-response associations was developed to help organize and communicate complex ecological information to support coral reef conservation. This study applied the Biological Condition Gradient (BCG), initially developed for freshwater ecosystems, to fish assemblages of U.S. Caribbean coral reef ecosystems. The reef fish BCG describes how biological conditions changed incrementally along a gradient of increasing anthropogenic stress. Coupled with physical and chemical water quality data, the BGC forms a scientifically defensible basis to prioritize, protect and restore water bodies containing coral reefs. Through an iterative process, scientists from across the U.S. Caribbean used fishery-independent survey data and expert knowledge to develop quantitative decision rules to describe six levels of coral reef ecosystem condition. The resultant reef fish BCG provides an effective tool for identifying healthy and degraded coral reef ecosystems and has potential for global application.

The use of multiscale stressors with biological condition assessments: A framework to advance the assessment and management of streams

Incorporating information on landscape condition (or integrity) across multiple spatial scales and over large spatial extents in biological assessments may allow for a more integrated measure of stream biological condition and better management of streams. However, these systems are often assessed and managed at an individual scale (e.g., a single watershed) without a larger regional multiscale context. In this paper, our goals were: (1) To develop a conceptual framework that could combine stream biological condition to abiotic landscape integrity (or, conversely, stressor) data at three spatial scales: watershed, catchment and stream-reach scale, to enable more targeted management actions. Measures of landscape integrity and stressors are negatively related, i.e., integrity on a 0-1 scale is equal or equivalent to stressors on a 1-0 scale. (2) To develop the framework in such a way that allows operational flexibility, whereby different indicators can be used to represent biological condition, and landscape integrity (or stressors) at various scales. (3) To provide different examples of the framework's use to demonstrate the flexibility of its application and relevance to management. Examples include stream biological assessments from different regions and states across the U.S. for fish, macroinvertebrates and diatoms using a variety of assessment tools (e.g., the Biological Condition Gradient (BCG), and an Index of Biotic Integrity (IBI)). Landscape integrity indicators comprise U.S. EPA's nationally available Index of Watershed Integrity (IWI) and Index of Catchment Integrity (ICI), and state and regional derived watershed and stream-reach scale integrity indicators. Scatterplots and a landscape integrity map were used to relate samples of stream condition classes (e.g., good, fair, poor) to watershed, catchment and stream-reach scale integrity. This framework and approach could provide a powerful tool for prioritizing, targeting, and communicating management actions to protect and restore stream habitats, and for informing the spatial extent at which management is applied.

Biologia Futura: integrating freshwater ecosystem health in water resources management

Sustainable water use implies the simultaneous protection of water quality and quantity. Beyond their function to support human needs such as drinking water provision, transportation and recreation freshwater bodies are also habitats. Conceiving them as water users on their own with respective biological, physico-chemical and morphological requirements could help maintaining their healthy state. Healthy freshwater ecosystems are also attractive for high-value human uses. Dwindling per capita availability of water, increasing demands, human well-being and climate change lead to competition for, and pressures on freshwater ecosystems. This has been conceptualized through the modification of the drivers–pressures–state–impacts–responses framework. This distinguishes between pressures, associated with the achievement of human well-being, and stressors, which are defined as the negative effect of excessive pressures or combination thereof on aquatic ecosystems. Guidelines usually specify threshold values to classify water bodies as appropriate for certain utilitarian uses. However, only few guidelines focus on freshwater ecosystem health. Eight guidelines for monitoring of freshwater ecosystem health were analysed in the UNEP-funded project “International Water Quality Guidelines for Ecosystems”. Based on this review, general benchmark values are proposed for key physico-chemical indicators. Furthermore, adaptive pathways towards improved monitoring and protection of the health of freshwater ecosystems are recommended. In this paper, we review the main findings of the report and also review its recent uptake. Water quality guidelines for freshwater ecosystems cannot be conceived without societal consensus and vision. Different climatic, geographical and socioeconomic contexts are to be considered too. Their development is embedded in an adaptive cycle. Its multiple phases and steps indicate a long-term approach including reassessment and potential revisions.

Choice of field and laboratory methods affects the detection of anthropogenic disturbances using stream macroinvertebrate assemblages

Accurate and precise detection of anthropogenic impacts on stream ecosystems using macroinvertebrates as biological indicators depends on the use of appropriate field and laboratory methods. We assessed the responsiveness to anthropogenic disturbances of assemblage metrics and composition by comparing commonly employed alternative combinations of field sampling and individuals counting methods. Four datasets were derived by, in the field 1) conducting multihabitat sampling (MH) or 2) targeting samples in leaf packs (single-habitat sampling - SH) and, in the laboratory A) counting all individuals of the samples, or B) simulating subsampling of 300 individuals per sample. We collected our data from 39 headwater stream sites in a drainage basin located in the Brazilian Cerrado. We used a previously published quantitative integrated disturbance index (IDI), based on both local and catchment disturbance measurements, to characterize the intensity of anthropogenic alterations at each site. Family richness and % Ephemeroptera, Plecoptera and Trichoptera (% EPT) individuals obtained from each dataset were tested against the IDI through simple linear regressions, and the differences in assemblage composition between least- and most-disturbed sites was tested using Permutational Multivariate Analysis of Variance (PERMANOVA). When counting all individuals, differences in taxonomic richness and assemblage composition of macroinvertebrate assemblages between least- and most-disturbed sites were more pronounced in the MH than in the SH sampling method. Leaf packs seemed to concentrate high abundance and diversity of macroinvertebrates in highly disturbed sites, acting as 'biodiversity hotbeds' in these situations, which likely reduced the response of the assemblages to the disturbance gradient when this substrate was targeted. However, MH sampling produced weaker results than SH when subsampling was performed. The % EPT individuals responded better to the disturbance gradient when SH was employed, and its efficiency was not affected by the subsampling procedure. We conclude that no single method was the best in all situations, and the efficiency of a sampling protocol depends on the combination of field and laboratory methods being used. Although the total count of individuals with multihabitat sampling obtained the best results for most of the evaluated variables, the decision of which procedures to use depends on the amount of time and resources available, on the variables of interest, on the availability of habitat types in the sites sampled, and on the other methods being employed in the sampling protocol.

Mazor R, Theroux S, J. Gillett D, Lane B, Gearheart G. The importance of open science for biological assessment of aquatic environments

Open science principles that seek to improve science can effectively bridge the gap between researchers and environmental managers. However, widespread adoption has yet to gain traction for the development and application of bioassessment products. At the core of this philosophy is the concept that research should be reproducible and transparent, in addition to having long-term value through effective data preservation and sharing. In this article, we review core open science concepts that have recently been adopted in the ecological sciences and emphasize how adoption can benefit the field of bioassessment for both prescriptive condition assessments and proactive applications that inform environmental management. An example from the state of California demonstrates effective adoption of open science principles through data stewardship, reproducible research, and engagement of stakeholders with multimedia applications. We also discuss technical, sociocultural, and institutional challenges for adopting open science, including practical approaches for overcoming these hurdles in bioassessment applications.

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function

Background

Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad “aquascape” scale, and few if any have applied the newest nanopore technology.

Results

We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5–1.0 ⋅ 10⁶ long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers.

Conclusions

Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.

Changes in invertebrate community composition allow for consistent interpretation of biodiversity loss in ecological status assessment

Biological communities change in response to human alteration. The response of individual taxa and the community can be used to establish preventive criteria to halt further biodiversity deterioration. Here we explore how consistent are the boundaries between Good and Moderate ecological status derived from classification systems used in North-NW Spain: NORThern Spain Indicators system (NORTI), River type specific multimetric (METI) and Iberian Bio-monitoring Working Party (IBMWP), by using common interpretation of normative definitions of Water Framework Directive. We applied the three classifications to a monitoring dataset of Nalón River basin, comprising samples from different stream types and reference conditions. We applied Threshold Indicator Taxa ANalysis to the invertebrate community along the most relevant environmental pressures and biological impairment gradients represented by the Ecological Quality Ratio (EQR) scores of the classification systems. Only NORTI provided a true community ecological threshold and the change point (cp) 95% quantile (Q95%) range of 0.760 was assumed to be the boundary from Good to Moderate (G/M) status, used to standardize the number of taxa loss in all systems. Since the average number of taxa at reference sites was 34, the estimated loss of sensitive taxa was up to 97.1% in IBMWP, 73.5% in METI and 52.9% in NORTI when passing from Good to Moderate status, revealing very permissive boundaries. The loss of common sensitive taxa in NORTI at Q95% was used as G/M threshold and applied to the other classifications, resulting all in a common biodiversity loss of 21% of sensitive taxa richness at values of NORTI-EQR = 0.760, METI-EQR = 0.818 and IBMWP-EQR = 0.753. Results indicate that significant community changes along pressure gradients allow for establishing quantitative criteria consistent with normative definitions. This understanding derived from Directive monitoring programs can assess the risk that invertebrate communities face in terms of species loss derived from anthropogenic pressures.

Managing estuaries for ecosystem function

Estuary management is limited by lack of consensus on operational tools for handling multiple conflicting management objectives. One critical step to this goal is a shift from individual problems to a focus on maintaining ecosystem functions that benefit humans. If function is maintained, then the ecosystem is said to be functionally equivalent to its unimpacted state, which is sufficient for management. We propose an adaptation of a functional equivalency (FE) assessment approach from marine fishery management and use a case study demonstration to address how this approach can be integrated into existing ecosystem assessment tools. The functional equivalency framework has three components for implementation: definition of target ecosystem functions, measurable metrics of ecosystem functions, and policy-based thresholds for each metric that indicate when functional equivalency is lost and must be restored. Each case study is an application of available data, models, and management policy to define these ecosystem function components. We intend to foster discussion and future work on integrating the FE approach into existing ecosystem assessment tools. Data requirements are high, as is the necessary integration between science and policy. The results can be a more integrated management approach focused on maintenance of ecosystem functions most beneficial to humans.

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.

The importance of natural versus human factors for ecological conditions of streams and rivers

Streams are influenced by watershed-scale factors, such as climate, geology, topography, hydrology, and soils, which mostly vary naturally among sites, as well as human factors, agriculture and urban development. Thus, natural factors could complicate assessment of human disturbance. In the present study, we use structural equation modeling and data from the 2008-2009 United States National Rivers and Streams Assessment to quantify the relative importance of watershed-scale natural and human factors for in-stream conditions. We hypothesized that biological condition, represented using a diatom multimetric index (MMI), is directly affected by in-stream physicochemical environment, which in turn is regulated by natural and human factors. We evaluated this hypothesis at both national and ecoregion scales to understand how influences vary among regions. We found that direct influences of in-stream environment on diatom MMIs were greater than natural and human factors at the national scale and in all but one ecoregion. Meanwhile, in-stream environments were jointly explained by natural variations in precipitation, base flow index, hydrological stability, % volcanic rock, soil water table depth, and soil depth and by human factors measured as % crops, % other agriculture, and % urban land use. The explained variance of in-stream environment by natural and human factors ranged from 0.30 to 0.75, for which natural factors independently accounted for the largest proportion of explained variance at the national scale and in seven ecoregions. Covariation between natural and human factors accounted for a higher proportion of explained variance of in-stream environment than unique effects of human factors in most ecoregions. Ecoregions with relatively weak effects by human factors had relatively high levels of covariance, high levels of human disturbance, or small ranges in human disturbance. We conclude that accounting for effects of natural factors and their covariation with human factors will be important for accurate ecological assessments.

Incorporating functional traits to enhance multimetric index performance and assess land use gradients

Taxonomic-based multimetric indices (MMIs) have been widely employed for assessing ecosystem status, particularly through the use of stream macroinvertebrate assemblages. However, the functional diversity and composition of assemblages is also important for maintaining stream ecosystem condition. Nonetheless, aquatic insect functional diversity and composition have not commonly been included in MMIs. Our goal was to advance our understanding of the performance and ecological interpretation of an MMI that potentially combined functional and taxonomic metrics. We sampled aquatic insects and natural and land-use variables at 74 temperate Chinese streams. We selected a candidate set of 36 functional and 20 taxonomic metrics that were screened by range tests, natural variation, responsiveness to anthropogenic disturbance, and redundancy for subsequent inclusion in MMIs. We determined if natural variation adjustments improved the performance of a functional-taxonomic MMI. Finally, we evaluated the degree to which the functional-taxonomic MMI served as an early-warning indicator of land use intensity. Natural variation explained between 19.62% and 71.02% of metric variability, indicating that functional metrics changed systematically along natural gradients. The final functional-taxonomic MMI adjusted for natural variation incorporated multiple aspects of assemblage characteristics: functional richness, Rao's quadratic entropy, abundance-weighted frequency of soft bodies, abundance-weighted frequency of predators, and number of Diptera taxa. In contrast to the natural variation unadjusted MMI, the functional-taxonomic adjusted MMI clearly distinguished least-disturbed sites from most-disturbed sites, exhibited high precision and low bias, and showed a significant negative response to land uses. The slope of a linear regression relative to 0-10% urban and 0-20% agriculture was significantly steeper for the functional-taxonomic adjusted MMI than that of the taxonomic adjusted MMI. We conclude that functional-taxonomic adjusted MMIs are more effective indicators of ecological condition and risks to biota from human pressures than are purely taxonomic unadjusted MMIs because functional-taxonomic MMIs are more sensitive to subtle anthropogenic pressures.

Establishing nutrient thresholds in the face of uncertainty and multiple stressors: A comparison of approaches using simulated datasets

Various methods have been proposed to identify threshold concentrations of nutrients that would support good ecological status, but the performance of these methods and the influence of other stressors on the underlying models have not been fully evaluated. We used synthetic datasets to compare the performance of ordinary least squares, logistic and quantile regression, as well as, categorical methods based on the distribution of nutrient concentrations categorised by biological status. The synthetic datasets used differed in their levels of variation between explanatory and response variables, and were centered at different positions along the stressor (nutrient) gradient. In order to evaluate the performance of methods in "multiple stressor" situations, another set of datasets with two stressors was used. Ordinary least squares and logistic regression methods were the most reliable when predicting the threshold concentration when nutrients were the sole stressor; however, both had a tendency to underestimate the threshold when a second stressor was present. In contrast, threshold concentrations produced by categorical methods were strongly influenced by the level of the stressor (nutrient enrichment, in this case) relative to the threshold they were trying to predict (good/moderate in this instance). Although all the methods tested had limitations in the presence of a second stressor, upper quantiles seemed generally appropriate to establish non-precautionary thresholds. For example, upper quantiles may be appropriate when establishing targets for restoration, but not when seeking to minimise deterioration. Selection of an appropriate threshold concentration should also attend to the regulatory regime (i.e. policy requirements and environmental management context) within which it will be used, and the ease of communicating the principles to managers and stakeholders.

Relationships between diatom metrics based on species nutrient traits and agricultural land use

We assessed how diatom metrics were related to different ranges of agricultural land use. Diatom assemblage composition, nutrients, and landscape characteristics were determined at 232 sites in eight agriculturally dominated study areas of the continental United States. Two regional groups based on differences in diatom relations to human disturbance were determined. Changes in diatom species composition were related to nutrients, pH, and conductivity in the eastern study areas (due to more wetlands) and more exclusively to nutrients in the west-central study areas. Homogenization of diatom flora among streams was related to high agricultural disturbance at this transcontinental scale. Species traits were developed separately for the east and west-central study groups and calculated two ways: indicator species analysis for taxa in low and high TN or TP conditions and weighted average partial least squares models of TN and TP concentration. These diatom metrics were significantly related to many indicators of agricultural land use in watersheds, especially percent row crops. Further analysis was conducted on only the west-central region due to its larger sample size. Overall, diatom metrics using species responses to N gradients were better related to agricultural land use than were species responses to P gradients. Most nutrient-based diatom metrics changed greatly in response to low ranges of percent row crops, but only a few high N diatom metrics responded to high row crop conditions. The greater response of diatoms to changes in low agriculture conditions may be due to past diatom evolution occurring when most waters had low nutrient conditions.

Management of headwaters based on macroinvertebrate assemblages and environmental attributes

The ecosystem function of headwaters is important and increasingly well-recognized, but institutional structures to administer their protection and management are lacking or poorly developed. Although the reasons for this mismatch are various, one of practical concern is the potential administrative burden imposed by the sizable number of headwaters. Two essential components of an administrative framework for managing waters is classification by type so that proper expectations can be set, and development of indicators that measure whether those expectations are being met. Ordinations of macroinvertebrate assemblages sampled from 1016 sites in 934 headwater streams draining <13 km² across Ohio, USA, revealed a highly distinct subset of sites characterized by a combination of taxa having an affinity for cold water and sensitivity to environmental disturbance. Bayesian Network (BN) modeling revealed that several environmental variables, notably water temperature, percent forest cover, and drainage area predict membership in this subset. More generally across all streams, macroinvertebrate assemblages signaled ecological status along a stressor gradient defined by habitat quality and intensity of land uses. Collectively, these results suggest a hierarchical administrative framework wherein stream habitat quality, as measured by summary habitat index scores, can screen and assign protections to waters generally expected to support assemblages consistent with good ecological status. Forest cover and water temperature can serve as an additional screen to assign higher levels of protection consistent with higher ecological status. In cases where levels of protection based on screening are questioned or likely to be contentious, assessment of the macroinvertebrate assemblage can demonstrate the appropriate level.

Linking the Agricultural Landscape of the Midwest to Stream Health with Structural Equation Modeling

Multiple physical and chemical stressors can simultaneously affect the biological condition of streams. To better understand the complex interactions of land-use practices, water quality, and ecological integrity of streams, the U.S. Geological Survey National Water Quality Assessment Project is conducting regional-scale assessments of stream condition across the United States. In the summer of 2013, weekly water samples were collected from 100 streams in the Midwestern United States. Employing watershed theory, we used structural equation modeling (SEM) to represent a general hypothesis for how 16 variables (previously identified to be important to stream condition) might be inter-related. Again, using SEM, we evaluated the ability of this "stressor network" to explain variations in multimetrics of algal, invertebrate, and fish community health, trimming away any environmental variables not contributing to an explanation of the ecological responses. Seven environmental variables-agricultural and urban land use, sand content of soils, basin area, percent riparian area as forest, channel erosion, and relative bed stability-were found to be important for all three-community metrics. The algal and invertebrate models included water-chemistry variables not included in the fish model. Results suggest that ecological integrity of Midwest streams are affected by both agricultural and urban land uses and by the natural geologic setting, as indicated by the sand content of soils. Chemicals related to crops (pesticides and nutrients) and residential uses (pyrethroids) were found to be more strongly related to ecological integrity than were natural factors (riparian forest, watershed soil character).

Biological Assessment of Coral Reefs in Southern Puerto Rico: A Technical Approach for Coral Reef Protection Under the U.S. Clean Water Act

States and other jurisdictions may protect coral reefs using biological water quality standards outlined by the United States Clean Water Act (CWA). Such protection will require long-term, regional monitoring of the resource using biological indicators and a probability-based sampling design. A 60-station survey targeting nearshore linear coral reef was conducted across southern Puerto Rico in December 2011 to document the status of reef inhabitants using a probabilistic, regional sampling design. The quantity, type and condition of stony corals, fish, gorgonians and sponges were documented from each station, providing a robust representation of linear reef status and composition across the region. Fish represented 106 unique taxa and stony corals 32 unique taxa. Benthic organisms (stony corals, sponges and gorgonians) averaged nearly 12 colonies per square meter, more than half of which were gorgonians. Assessment results can be used as a baseline to compare with future regional surveys to quantify change in reef condition over time (trend). Both temporal and spatial changes can be expected after large-scale disturbances like hurricanes Maria and Irma in 2017. The indicators and probabilistic sampling design support the long-term regional monitoring envisioned by the Environmental Protection Agency to implement CWA protections in Puerto Rico and elsewhere.

Resolving taxonomic ambiguities: effects on rarity, projected richness, and indices in macroinvertebrate datasets

Biodiversity information is an important basis for ecological research and environmental assessment, and can be impacted by choices made in the manipulation and analysis of taxonomic data. Such choices include methods for resolving multiple redundant levels of taxonomic resolution, as typically arise with morphological identification of damaged or immature aquatic macro-invertebrates. In particular, the effects of these processing choices on number of rare taxa are poorly understood yet potentially significant to the estimation of projected taxa richness and related evaluations such as biodiversity conservation value and survey sufficiency. Using aquatic macroinvertebrate data collected for two nearshore areas of Lake Superior, we determined how multiple methods of resolving taxonomic redundancies influence two commonly-used estimates of projected richness, Chao1 and Chao2, which hinge on the ratio of taxa that are singletons to doubletons (i.e., just one versus two individuals found) or uniques versus duplicates (i.e., just one versus two occurrences). We also determined how choice of ambiguous taxa method, including some modified specifically to retain rare taxa and others taken from the literature, influenced effort to reach 95% of projected richness, site-level richness and abundance, and representative invertebrate IBI scores. We found that Chao1 was more sensitive to method choice than Chao2, because singleton and doubleton status was more frequently affected when taxa were deleted, merged, or re-assigned in the process of resolving taxonomic redundancies than was unique and duplicate status. Methods that eliminated redundant taxa at the site scale but not the study-area scale tended to overinflate study area and projected richness, and resulted in a significant loss of abundance. The method that aggregated or deleted redundant taxa depending on abundance resulted in a decrease in site and study area richness, abundance, and an underestimation of projected richness. Methods which re-assigned parents to common children retained a majority of richness and abundance information and a more realistic estimate of projected taxa richness; however, the identity of poorly-identified parents was imputed. All methods resulted in little effect to typical IBI scores. Overall, no one method is fully capable of removing spurious richness at the study-area scale while preserving all taxa occurrence, abundance and rarity patterns. Therefore, the most appropriate method for making comparisons among sites may be different than the most appropriate method for comparing among surveys or among study areas, or if a goal is to estimate projected taxa richness or retain rare taxa information.

Diatom Assemblage Changes in Agricultural Alluvial Plain Streams and Application for Nutrient Management

In large, alluvial floodplains dominated by agriculture, small streams have the potential to experience nutrient enrichment affecting algal assemblage structure and metabolism. Nutrient enrichment is largely driven by application of nutrients and altered hydrologic regimes. To inform stressor-response-based nutrient reduction goals for agricultural alluvial plain streams, diatom assemblages were sampled from 25 streams located within the Mississippi Alluvial Plain (MAP) with various land management practices and associated P and N inputs. From August through September 2015, epidendric diatom assemblage samples were collected from instream woody debris. Field nutrient gradients were skewed toward higher concentrations, and ranges of previously reported diatom assemblage response thresholds indicative of oligotrophic conditions were not well represented. Ordination analysis identified a gradient in species composition associated with increasing P and decreasing dissolved oxygen. A significant shift in diatom assemblage structure occurred when total P concentrations in the MAP streams exceeded 0.12 mg L-. Phosphorus-enriched systems were represented by a distinct set of indicator species, lower abundances of ubiquitous species, greater abundances of highly tolerant species, and greater abundances of high-P indicator species. No relationships were observed among diatom assemblage measures or traits with increasing N. Current results do not address potential criteria for identifying high-quality, oligotrophic streams. However, measures of diatom assemblage structure have potential for helping set benchmarks to reduce nutrient impacts and monitor effects of agricultural best management practices on MAP streams.

Development of a benthic macroinvertebrate multimetric index for large semiwadeable rivers in the Mid-Atlantic region of the USA

To meet the objective of protecting water quality standards outlined in the US Clean Water Act, many agencies and organizations have created standardized biological assessment methods to evaluate aquatic ecosystem integrity. However, few Mid-Atlantic states have assessment methods specifically designed for rivers with drainage areas ≥ 2600 km². Most rivers in this region fall into a semiwadeable category, where both wadeable and nonwadeable biological collection methods are difficult to implement. Additionally, these rivers often transcend state boundaries, which hinder consistent assessment determinations between states. Consequently, we developed a benthic macroinvertebrate assessment tool using a modified wadeable collection method for large semiwadeable rivers that can be used across state lines. Our results indicate that the two multimetric indices we developed (summer and autumn) are uniquely effective at distinguishing between least disturbed and stressed environmental conditions.

Advancing evaluation of bioassessment methods: A reply to Liu and Cao

A series of three papers was written about the development of multimetric indices (MMIs) using diatoms in rivers, streams and lakes for transcontinental surveys conducted by the United States Environmental Protection Agency. Stevenson et al. (2013) used the surface sediment diatom data from the 2007 National Lake Assessment to develop national scale site specific models for MMIs to account for natural variation in condition among sites. Liu and Stevenson (2017) also used the 2007 lakes data to evaluate performance of MMIs by grouping sites by ecoregions or typologies (naturally similar types of lakes defined by similarity in diatom species composition) with site specific metric models (SSMMs) that adjust metrics for natural variability among sites. Tang et al. (2016) used benthic diatom data from the 2008-2009 National River and Stream Assessment to develop SSMMs and MMIs by ecoregion and typology. All three studies showed that SSMMs improved performance of diatom MMIs by accounting for natural variation among sites. None of the studies provided consistent evidence that grouping sites by typologies produced better MMI performance than grouping sites by ecoregions. Liu and Cao (2018) criticized the Tang et al. (2016) paper for using means and standard errors to evaluate relative performance of MMI calculation methods at the site group scale, however, their criticism is incorrect. Actually, Tang et al. (2016) only used means to summarize and report relative performance of MMI calculation methods in the body of the paper. Tang et al. (2016) appropriately used non-parametric rank sum approaches to evaluate the probability that the multiple MMI calculations for separate site groups were the same for ecoregion (n = 9) and typology (n = 7) site groups. Liu and Stevenson (2017) used this same non-parametric approach for tests of lake diatom MMIs. Liu and Cao's (2018) concerns can be addressed by distinguishing between the goals and methods used for testing and evaluation of MMI calculation methods at the national and site-group scales. Tang et al. (2016) did not aggregate data across site groups to test MMI performance at the national scale because they were following standard EPA methods that develop separate MMIs for each site group. In conclusion, Liu and Cao (2018) misunderstood the MMI evaluation in Tang et al. (2016) and added no new information to this body of work, because all the concerns they raised were discussed in Liu and Stevenson (2017).

An Adaptive Environmental Effects Monitoring Framework for Assessing the Influences of Liquid Effluents on Benthos, Water, and Sediments in Aquatic Receiving Environments

Environmental effects monitoring (EEM) has been traditionally used to evaluate the effects of existing facilities discharging liquid effluents into natural receiving waters in Canada. EEM also has the potential to provide feedback to an ongoing project in an adaptive management context and can inform the design of future projects. EEM, consequently, can and should also be used to test the predictions of effects related to new projects. Despite EEM's potential for widespread applicability, challenges related to the effective implementation of EEM include the use of appropriate study designs and the adoption of tiers for increasing or decreasing monitoring intensity. Herein we describe a template for designing and implementing a 6-tiered EEM program that utilizes information from the project-planning and predevelopment baseline data collection stages to build on forecasts from the initial environmental impact assessment project-design stage and that feeds into an adaptive management process. Movement between the 6 EEM tiers is based on the exceedance of baseline monitoring triggers, forecast triggers, and management triggers at various stages in the EEM process. To distinguish these types of triggers, we review the historical development of numeric and narrative triggers as applied to chemical (water and sediment) and biological (plankton, benthos, fish) endpoints. We also provide an overview of historical study design issues and discuss how the 6 EEM tiers and associated triggers influence the temporal-spatial experimental design options and how the information gained through EEM could be used in an adaptive management context. Integr Environ Assess Manag 2018;14:552-566. © 2018 SETAC.

A stream classification system to explore the physical habitat diversity and anthropogenic impacts in riverscapes of the eastern United States

Describing the physical habitat diversity of stream types is important for understanding stream ecosystem complexity, but also prioritizing management of stream ecosystems, especially those that are rare. We developed a stream classification system of six physical habitat layers (size, gradient, hydrology, temperature, valley confinement, and substrate) for approximately 1 million stream reaches within the Eastern United States in order to conduct an inventory of different types of streams and examine stream diversity. Additionally, we compare stream diversity to patterns of anthropogenic disturbances to evaluate associations between stream types and human disturbances, but also to prioritize rare stream types that may lack natural representation in the landscape. Based on combinations of different layers, we estimate there are anywhere from 1,521 to 5,577 different physical types of stream reaches within the Eastern US. By accounting for uncertainty in class membership, these estimates could range from 1,434 to 6,856 stream types. However, 95% of total stream distance is represented by only 30% of the total stream habitat types, which suggests that most stream types are rare. Unfortunately, as much as one third of stream physical diversity within the region has been compromised by anthropogenic disturbances. To provide an example of the stream classification’s utility in management of these ecosystems, we isolated 5% of stream length in the entire region that represented 87% of the total physical diversity of streams to prioritize streams for conservation protection, restoration, and biological monitoring. We suggest that our stream classification framework could be important for exploring the diversity of stream ecosystems and is flexible in that it can be combined with other stream classification frameworks developed at higher resolutions (meso- and micro-habitat scales). Additionally, the exploration of physical diversity helps to estimate the rarity and patchiness of riverscapes over large region and assist in conservation and management.

Identifying non-reference sites to guide stream restoration and long-term monitoring

The reference condition paradigm has served as the standard for assessing the outcomes of restoration projects, particularly their success in meeting project objectives. One limitation of relying solely on the reference condition in designing and monitoring restoration projects is that reference conditions do not necessarily elucidate impairments to effective restoration, especially diagnosing the causal mechanisms behind unsuccessful outcomes. We provide a spatial framework to select both reference and non-reference streams to guide restoration planning and long-term monitoring through reliance on anthropogenically altered ecosystems to understand processes that govern ecosystem biophysical properties and ecosystem responses to restoration practices. We then applied the spatial framework to East Fork Poplar Creek (EFPC), Tennessee (USA), a system receiving 30years of remediation and pollution abatement actions from industrialization, pollution, and urbanization. Out of >13,000 stream reaches, we identified anywhere from 4 to 48 reaches, depending on the scenario, that could be used in restoration planning and monitoring for specific sites. Preliminary comparison of fish species composition at these sites compared to EFPC sites were used to identify potential mechanisms limiting the ecological recovery following remediation. We suggest that understanding the relative role of anthropogenic pressures in governing ecosystem responses is required to successful, process-driven restoration.

Macroinvertebrate communities in riverine systems of buffer areas of protected wildland, rangeland and city areas: implications for conservation of riverine systems on urbanising watersheds

Riverine systems in developing countries continue to be degraded by anthropogenic pressures such as urbanisation. The responses of biota in watersheds surrounding a drainage divide may provide critical information that is required to protect the ecological condition of riverine systems. This study assessed the spatial variation of selected environmental variables together with macroinvertebrate communities in upper reaches of riverine systems across different land use categories of the Bulawayo region. Based on an a priori selection criterion, studied sites were grouped following an urban-wastewater disturbance gradient comprising of (i) heavily polluted city sites, (ii) moderately disturbed rangeland sites and (iii) less disturbed sites of the buffer areas of protected wildland. Most of the studied environmental variables and the macroinvertebrate community assemblages were significantly (ANOVA, p < 0.05) different and degraded within the city areas. In this study, the variance of environmental variables known to be associated with organic pollution like increased nutrients, embeddedness by particulates, salinity, COD, conductivity, turbidity and reduced dissolved oxygen was found to be related with the variation of macroinvertebrate communities across the studied sites. Besides affirming the effectiveness of macroinvertebrate-based bioassessment approaches, the results of our study demonstrate that an aggressive riverine protection policy that prohibits the discharge of poor-quality urban effluents and preservation of the less disturbed riverine systems needs to be part of the larger urban planning and regulatory framework in urbanising watersheds.

Improving assessment accuracy for lake biological condition by classifying lakes with diatom typology, varying metrics and modeling multimetric indices

Site grouping by regions or typologies, site-specific modeling and varying metrics among site groups are four approaches that account for natural variation, which can be a major source of error in ecological assessments. Using a data set from the 2007 National Lakes Assessment project of the USEPA, we compared performances of multimetric indices (MMI) of biological condition that were developed: (1) with different lake grouping methods, ecoregions or diatom typologies; (2) by varying or not varying metrics among site groups; and (3) with different statistical techniques for modeling diatom metric values expected for minimally disturbed condition for each lake. Hierarchical modeling of MMIs, i.e. grouping sites by ecoregions or typologies and then modeling natural variability in metrics among lakes within groups, substantially improved MMI performance compared to using either ecoregions or site-specific modeling alone. Compared with MMIs based on ecoregion site groups, MMI precision and sensitivity to human disturbance were better when sites were grouped by diatom typologies and assessing performance nationwide. However, when MMI performance was evaluated at site group levels, as some government agencies often do, there was little difference in MMI performance between the two site grouping methods. Low numbers of reference and highly impacted sites in some typology groups likely limited MMI performance at the group level of analysis. Varying metrics among site groups did not improve MMI performance. Random forest models for site-specific expected metric values performed better than classification and regression tree and multiple linear regression, except when numbers of reference sites were small in site groups. Then classification and regression tree models were most precise. Based on our results, we recommend hierarchical modeling in future large scale lake assessments where lakes are grouped by ecoregions or diatom typologies and site-specific metric models are used to establish expected metric values.