A multi‐metric fish index to assess the environmental condition of estuaries

The development of a multi‐metric fish index, the Estuarine Fish Community Index (EFCI), for assessing estuarine environments is described. The index comprises 14 metrics or measures that represent four broad fish community attributes: species diversity and composition, species abundance, nursery function and trophic integrity. The individual metrics were evaluated using data that were collected on a South African estuary that was degraded and in which rehabilitation measures were implemented. The evaluation suggested that the selected metrics adequately measure the condition of separate but related components of estuarine fish communities and that these reflect environmental condition. Reference conditions and metric thresholds were derived from fish community data collected during an extensive national study. The final multi‐metric index was then constructed and evaluated. The EFCI combines both structural and functional attributes of estuarine fish communities and integrates these to provide both a robust and sensitive method for assessing the ecological condition of estuarine systems. It is also an effective communication tool for converting ecological information into an easily understood format for managers, policy makers and the general public.     

Sensitivity analysis to explore responsiveness and dynamic range of multi-metric fish-based indices for assessing the ecological status of estuaries and lagoons

Fish-based multi-metric indices are an integral tool in implementing effective water policy initiatives for transitional waters. This study analysed the behaviour of three fish indices (TFCI in the UK, ELFI in France and EFAI in Portugal) developed for monitoring in line with the European Water Framework Directive, by applying a supervised multi-way sensitivity analysis with national monitoring data. The relative variation in the index outcome was analysed under different simulation scenarios by setting metric values at various levels and accounting for the co-variation between metrics. Subsets of key metrics were identified based on their higher influence in determining the index output. Index results under manipulations of metric scores clearly indicated that metric type, number of metrics used and correlations between metrics are important in determining their behaviour. This has implications for implementing management/conservation plans, for example, by prioritising restoration and/or conservation of metrics influencing more the ecological status. Indices including uncorrelated metrics (e.g. EFAI) or metrics with a skewed distribution (e.g. TFCI) are less affected by extreme metric changes, reducing the effectiveness of management actions aimed at improving the ecological status of a water body and thus adjustments may be needed to increase their sensitivity to changes in their metrics.     

Influence of sampling effort on metrics of fish-based indices for the assessment of estuarine ecological quality

Multimetric fish-based indices have been increasingly gaining importance in Europe, as the Water Framework Directive (WFD) requires fish fauna, and particularly its composition and abundance, to be taken into account in the assessment of the ecological quality of continental surface waters, including transitional waters. These indices are composed of several metrics, mostly related with structural and functional characteristics of fish communities, such as species richness, the role of nursery areas, or trophic web structure. Therefore, ecological quality assessments should ensure that these structural and functional characteristics of fish communities were covered by the sampling methods used. In the present work, the influence of sampling effort on several metrics of the Estuarine Fish Assessment Index (EFAI) was studied. Pseudo-random samples were generated from data of four Portuguese estuaries and bootstrap cycles were performed, in order to obtain metrics’ means and standard deviations per number of hauls analysed. The number of hauls necessary for the means to level off differed with the metrics considered. Generally, for metrics on percentages (percentage of marine migrants, percentage of estuarine residents and percentage of piscivores) the curve levelled off with less than 20 hauls, both for the estuary as a whole and for different estuarine salinity zones. On the other hand, metrics on species richness required much larger samples. In order to decrease to −5% the current estimated bias of metrics, the WFD sampling costs would have to be more than 3 times higher than they currently are. The findings in the present study are of great importance for an effective assessment of estuarine ecological quality and particularly in the context of the WFD, as the metrics studied are common to other Member State indices.     

Ecological assessment of soft bottom benthic communities in northern Spanish estuaries

The implementation of the Water Framework Directive requires the classification of the ecological quality status of benthic macroinvertebrates in costal and transitional waters. The uncertainty and complexity of this task have lead to the creation of specific Geographical Intercalibration Groups (GIGs) for the different ecoregions and types of water bodies established. In this framework, several metrics are under study in the United Kingdom, Spain and Denmark for North East Atlantic coastal waters (NEA-GIG). All of them include in their formulations the AMBI index. Nevertheless, few advances have been made in relation to transitional waters. This paper aims to test the suitability of those methodological procedures for their application in Northern Spanish estuaries. The results show evident divergences in classification of ecological status among methods, although the correlations of corresponding ecological quality ratios (EQRs) are good. Thus, we think that it may be necessary to modify the boundaries between each ecological status category and adjust the reference conditions for the variety of community-types existing in estuarine water bodies. However, some problems arise in the assessment of some naturally stressed communities. In this situation, we found an overall dominance of species tolerant to organic enrichment in all status categories and low range of variation of AMBI index. This aspect introduces some uncertainty in relation to the ability of this index to detect a deleterious effect in these estuarine communities naturally stressed. On the other hand, we found some sites that achieve good status according to the metrics used, even though the number of opportunistic species was high. The use of combined approaches that incorporate physicochemical condition of sediments would be a straightforward approach to reduce the risk of failing in the assignation of ecological status category.     

Ecological status assessment of European lakes: a comparison of metrics for phytoplankton, macrophytes, benthic invertebrates and fish

Data on phytoplankton, macrophytes, benthic invertebrates and fish from more than 2000 lakes in 22 European countries were used to develop and test metrics for assessing the ecological status of European lakes as required by the Water Framework Directive. The strongest and most sensitive of the 11 metrics responding to eutrophication pressure were phytoplankton chlorophyll a, a taxonomic composition trophic index and a functional traits index, the macrophyte intercalibration taxonomic composition metric and a Nordic lake fish index. Intermediate response was found for a cyanobacterial bloom intensity index (Cyano), the Ellenberg macrophyte index and a multimetric index for benthic invertebrates. The latter also responded to hydromorphological pressure. The metrics provide information on primary and secondary impacts of eutrophication in the pelagic and the littoral zone of lakes. Several of these metrics were used as common metrics in the intercalibration of national assessment systems or have been incorporated directly into the national systems. New biological metrics have been developed to assess hydromorphological pressures, based on aquatic macrophyte responses to water level fluctuations, and on macroinvertebrate responses to morphological modifications of lake shorelines. These metrics thus enable the quantification of biological impacts of hydromorphological pressures in lakes.     

Development of an Angiosperm Quality Assessment Index (AQuA-Index) for ecological quality evaluation of Portuguese water bodies—A multi-metric approach

Salt marsh vegetation is one important biological element for establishing the ecological quality status (EQS) while evaluating transitional waters (TW). This intertidal plant community is sensitive to the most important pressures present in estuaries. In this study, an ecological index based multi-metric was established taking into account the species composition and ecological relations in Portuguese salt marsh habitats. During the AQuA-Index elaboration it was found that the parameters that respond better to the variability of ecological conditions present nowadays are the Shannon Diversity Index, the Shannon Maximum Diversity Index, the number of halophytic species, the Margalef Diversity Index and the Pielou Equitability Index. The application of the AQuA-Index index to eight TW systems varying in morphology and pressures, demonstrated that the metric responds to the ecological quality of each system. Also, it showed some advantages in comparison with other approaches, in zones with a relevant proportion of middle and upper marsh and where historical data were not available. This way the AQuA-Index proved to be an efficient Index for ecological quality assessment, using salt marsh vegetation as indicator.     

Implementation of a new index to assess intertidal seaweed communities as bioindicators for the European Water Framework Directory

An index CCO (cover, characteristic species, opportunistic species) has been developed for the implementation of the European Water Framework Directory (WFD) in coastal waters, using intertidal macroalgal communities as bio-indicator (Biological Quality Element). CCO is based on the calculation of three metrics corresponding to the global cover of macroalgal communities (metric 1), the number of characteristic species per topographic level/seaweed community (metric 2) and the cover of opportunistic species (metric 3). The final rating is obtained by pooling the scores of the three metrics. Results are given for 32 sites in 29 water bodies, grouped into four biogeographic regions along the Channel–Atlantic coasts of France. Over the six-year study, most of sites were sampled twice each (every three years). CCO index revealed that 25 coastal water bodies of both the Channel and the Bay of Biscay were in good or high ecological quality status (EQS), whereas only 4 of them were moderate and none in poor to bad status. However, significant differences have been found between sites and between geographic regions, water bodies located in Brittany obtaining the best EQS. No significant change occurred between the three-year sampling sets. A significant correlation has been established between a three-component anthropogenic pressure index and CCO ratings, showing the accuracy of CCO to evaluate the impact of anthropic activities on the structure and development of macroalgal communities as indicator of the ecological quality of coastal water bodies.     

Marine angiosperm indices used to assess ecological status within the Water Framework Directive and South African National Water Act: Learning from differences and common issues

This paper reviews and discusses the methods and metrics used for the assessment of the ecological status of marine angiosperms comparing the European with the South African situation. In Europe salt marsh and seagrasses are an important biological element for establishing the ecological quality status of transitional waters and in South Africa changes over time in the salt marsh and submerged macrophyte habitats (species richness, abundance and community composition) is used nationally to assess the health of estuaries. In Europe several studies have developed metrics that include salt marsh species composition and community structure to assess the ecological quality status. Deviation of taxonomic composition and abundance from a reference situation is investigated. Multi-metric approaches have been shown to provide a more holistic view of the ecological status of the ecosystem. Many indices are highly dependent on historical data to assess the deviation from reference conditions. Within the WFD spirit one widely used approach for salt marsh assessment, the Best’s method, the baseline can be determined based on the first sampling effort, by the largest previously recorded size of the salt marsh or using the “maximum potential size” of the salt marsh from habitat prediction models. In South Africa all habitat below the 5 m contour line is considered estuary habitat and any land occupied here by agricultural or other developments is considered as a loss of habitat from the reference condition. For seagrasses European metrics are based on attributes from the community (e.g., taxonomic composition, epiphytes), the population (e.g., bed extent, shoots density), but also quantified at individual species (e.g., leaves length) or physiological levels (e.g., stable isotopic signatures). Seagrass habitats in South African estuaries are highly dynamic in response to floods and an understanding of this is needed before present ecological status can be assessed.     

A fish-based index for the assessment of the ecological quality of temperate lakes

A fish – based index for the assessment of the ecological quality of natural temperate lakes was developed, in accordance to the requirements of the Water Framework Directive (WFD) 2000/60/EC. As a case study, 11 natural lakes located at northern and western Greece were selected. Fish surveys were conducted during mid summer to mid autumn in 2010, 2011 and 2012 using Nordic gillnets and electrofishing. Environmental parameters and anthropogenic pressures were assessed for each lake. Fish species richness, abundance, trophic, reproductive and habitat functional guilds were used for extracting a set of 107 metrics, meeting the requirements of the WFD. All metrics were initially tested as candidates for the index development. A stepwise linear regression of each metric against environmental parameters (lake area, altitude, maximum depth, alkalinity) and anthropogenic pressures (drainage area covered by non-natural land uses – NNLC, water total phosphorus concentrations – TP, Lake Habitat Modification Score – LHMS) was initially conducted for ensuring pressure-response relationships. Reference conditions for each lake were estimated by the hindcasting procedure and the ecological quality for each lake was expressed as the ecological quality ratio (EQR) by a value ranging from 0 (poor quality) to 1 (excellent quality). Two fish fauna metrics, the relative numerical abundance of introduced species (Introduced_a) and the relative biomass of omnivorous species (OMNI_b) were finally extracted as the most significant, responding to LHMS and TP, respectively. The final index was expressed as the mean values of the EQRs of these two metrics. The multimetric fish index presented herein could serve as a tool for assessing the ecological quality of natural lakes at broad geographical scale and generally, in the Mediterranean temperate lakes with similar hydromorphological characteristics.     

A multimetric diatom index to assess the ecological status of coastal Galician rivers (NW Spain)

There are many rivers in northwest Spain as a consequence of the mountainous landscape and the granitic geology subjected to Atlantic influences. Water and epilithic diatoms samples were collected at 72 sites in Galicia flowing into the Atlantic Ocean and Cantabrian Sea in summer 2002–2003 and spring 2004. These sites included minimally disturbed sites, defined as reference sites, and impacted sites which were influenced by different human pressures. We used the diatom assemblages to calculate diatom indices using the Omnidia software, but we also developed new metrics based on the similarity of species composition in reference sites. The response of the metrics was tested in relation to physicochemical variables. We developed a diatom multimetric index (MDIAT) as a combination of metric values. The sensitivity of the MDIAT to organic and nutrient stressors supports the use of this index to classify the ecological status of Galician rivers. The MDIAT showed higher correlations with some variables and nutrients than the individual metrics. According to the MDIAT, 69% of the sites sampled in Galician coastal rivers achieve good ecological status. The MDIAT has been developed specifically for Galician granitic rivers (NW Spain), and has been intercalibrated at the European level in the Central Baltic Rivers GIG. Our study validates the application of this multimetric index to evaluate the water quality in coastal Galician rivers.     

Detecting benthic community differences: Influence of statistical index and season

An accurate assessment of estuarine condition is critical to determining whether there has been a change from baseline or ‘natural’ conditions; benthic communities are routinely used as an ecological endpoint to make this assessment. We addressed two issues, which arise when attempting to detect differences between benthic communities. The first is the varying sensitivity of metrics, e.g. one metric may not be able to detect differences between two communities where another metric can. The second is the influence of season on the detection of differences between benthic communities from different estuarine systems. In this study, benthic communities taken from depositional sites were sampled in three seasons, at three sites within two relatively pristine estuaries located in southern Massachusetts, USA. Statistical comparisons of benthic community data from the two estuaries were made using three common metrics: species richness, Shannon diversity and Bray–Curtis similarity indices. Significant community differences were found depending upon the index. The Bray–Curtis index, using permutation testing, was the only metric that detected differences between estuaries despite disparate seasonal sampling. This suggests that researchers do not need to be overly constrained to sampling in the same season when testing for differences in benthic communities between estuaries. Additionally, we propose an analytical method to identify anthropogenically impacted estuarine systems.     

Biogeography of benthic macroinvertebrates in estuaries along the Gulf of Mexico and western Atlantic coasts1,2

A multimetric fish Index of Biotic Integrity (IBI) was composed to assess the biotic integrity of Flandrian water bodies. As fish communities differ substantially between standing waters, running waters of the bream zone and running waters of the barbel zone, eight candidate metrics for each of these water types or zones were identified, representing three major classes of biological attributes. These are species richness and composition, fish condition and abundance, trophic composition. The metrics were tested and modified where needed. The IBI was applied throughout Flanders on 104 locations in standing waters, 500 locations in waters of the bream zone and 257 locations in waters of the barbel zone. Standing waters scored substantially different from running waters. Standing waters rarely contained no fish at all, but their fish communities were very often poor to very poor. Waters of the bream and barbel zone were often fishless (respectively 40% and 35% of all locations contain no fish), but the locations with fish usually scored reasonable to poor. Only 18.5% of all locations were classified as reasonable to excellent (IBI classes 4 or lower on a scale from 1 to 9) and were considered to satisfy the basic ecological quality demands. The Leie-, Dijle-, Dender- and Schelde-basins had a very poor quality (more than 50% of the locations contained no fish). The Maas-, Grote and Kleine Nete-basins scored rather well, with respectively, 44%, 48% and 68% of the locations achieving an IBI of 4 or lower. The IBI is a valuable and complementary tool to assess the ecological quality of water bodies as suggested in the proposal for a Water Framework Directive by the European Commission.     

A fish-based index of estuarine ecological quality incorporating information from both scientific fish survey and experts knowledge

In the Water Framework Directive (European Union) context, a multimetric fish based index is required to assess the ecological status of French estuarine water bodies. A first indicator called ELFI was developed, however similarly to most indicators, the method to combine the core metrics was rather subjective and this indicator does not provide uncertainty assessment. Recently, a Bayesian method to build indicators was developed and appeared relevant to select metrics sensitive to global anthropogenic pressure, to combine them objectively in an index and to provide a measure of uncertainty around the diagnostic. Moreover, the Bayesian framework is especially well adapted to integrate knowledge and information not included in surveys data. In this context, the present study used this Bayesian method to build a multimetric fish based index of ecological quality accounting for experts knowledge. The first step consisted in elaborating a questionnaire to collect assessments from different experts then in building relevant priors to summarize those assessments for each water body. Then, these priors were combined with surveys data in the index to complement the diagnosis of quality. Finally, a comparison between diagnoses using only fish data and using both information sources underlined experts knowledge contribution. Regarding the results, 68% of the diagnosis matched demonstrating that including experts knowledge thanks to the Bayesian framework confirmed or slightly modified the diagnosis provided by survey data but influenced uncertainty around the diagnostic and appeared especially relevant in terms of risk management.     

An approach to intercalibrate ecological classification tools using fish in transitional water of the North East Atlantic

A simple procedure to harmonise and intercalibrate eight national methods classifying the ecological status using fish in transitional waters of the North East Atlantic is described. These methods were initially intercalibrated and a new method recently developed was added to this exercise. A common human pressure index pre-classified the status of each water body in an independent way. Ecological class boundaries values were established according to the level of anthropogenic pressure using regression analyses. A simulated dataset was used to assess the level of agreement between the fish classification methods. Fleiss’ multi-rater kappa analysis indicated that boundary harmonisation was achieved; all classifications fell within one class of each other and class agreement between methods exceeded 70%. The use of a pressure index to establish boundary thresholds provides a practical method of defining and harmonizing the quality classes associated with human pressures, as required by the European Water Framework Directive.     

Regional fish community indicators of landscape disturbance to catchments of the conterminous United States

Biological assessments of river conditions are increasingly conducted at regional and continental scales that match the extent of large-scale river management efforts. Multimetric indices composed of biological community indicators are commonly used to assess ecological condition and indices have recently been applied in large regions. Methods for large-scale multimetric index creation emphasize repeatability, comparability across regions, and objective selection of candidate metrics. Here we used an extensive fish dataset to create a large pool of fish community metrics which were screened to create multimetric indices (MMIs) in eight ecoregions covering the conterminous U.S. Candidate metrics were tested for metric range, corrected for natural gradients using boosted regression trees, and then tested for repeatability and sensitivity to landscape disturbance. Temporally stable and repeatable metrics were then evaluated for redundancy and used to compose MMIs for each region. Our MMIs were significantly correlated to independently developed MMIs, accurately reproducing prior index values with moderate to high precision and little bias. Our study demonstrates the utility of boosted regression tree models for correcting metric values for natural abiotic gradients and shows that the order of screening tests has a potentially important influence on metric selection. The resultant regional indices and component metrics provide a basis for assessing condition and testing hypotheses about landscape influences on aquatic ecosystems at a national scale in the US.     

Development of a fish-based index to assess the eutrophication status of European lakes

The use of the CEN (European Committee for Standardization) standard method for sampling fish in lakes using multi-mesh gillnets allowed the collection of fish assemblages of 445 European lakes in 12 countries. The lakes were additionally characterised by environmental drivers and eutrophication proxies. Following a site-specific approach including a validation procedure, a fish index including two abundance metrics (catch per unit effort expressed as fish number and biomass) and one functional metric of composition (abundance of omnivorous fish) was developed. Correlated with the proxy of eutrophication, this index discriminates between heavily and moderately impacted lakes. Additional analyses on a subset of data from Nordic lakes revealed a stronger correlation between the new fish index and the pressure data. Despite an uneven geographical distribution of the lakes and certain shortcomings in the environmental and pressure data, the fish index proved to be useful for ecological status assessment of lakes applying standardised protocols and thus supports the development of national lake fish assessment tools in line with the European Water Framework Directive.     

Developing and applying a benthic index of estuarine condition for the Virginian Biogeographic Province

A benthic index of estuarine condition was constructed for the Virginian Biogeographic Province (from Cape Cod, Massachusetts, to the mouth of Chesapeake Bay, Virginia) with data collected during summers of 1990 through 1993 by the US EPA’s Environmental Monitoring and Assessment Program (EMAP). Forty-eight metrics, based on attributes of the macrobenthos, were considered for the index, including measures of biodiversity, community condition, individual health, functional organization, and taxonomic composition. Salinity was correlated significantly with some of the metrics. Therefore, some metrics were normalized for salinity. The data used to develop the index (the calibration data) included equal numbers of reference and degraded sites, distributed equally across three salinity zones (<5, 5–18, >18‰). An independent set of data was used for validation. Linear discriminant analysis identified combinations of metrics that could best discriminate reference from degraded sites. The targets for correct classification were 90% of the sites for the calibration data and 80% for the validation data. Six combinations of metrics were identified. The final index was based on the ecological interpretation and relevance of the individual metrics and the ability to meet the calibration and validation targets. The final index consisted of three metrics: a positive contribution from salinity-normalized Gleason’s D (a biodiversity metric), and negative contributions from two taxonomic composition metrics, abundances of spionid polychaetes and of salinity-normalized tubificid oligochaetes. The index correctly classified 87% of reference and 90% of degraded sites in the calibration data and 88% of reference and 81% of degraded sites in the validation data. The index correctly classified sites over the full range of salinity (tidal-fresh to marine waters) and across grain sizes (silt–clay to sand).     

海州湾及邻近海域冬季鱼类群落结构及其与环境因子的关系

根据2011年冬季在海州湾及邻近海域进行的渔业资源底拖网和环境调查数据,应用物种多样性指数和多元分析等方法,对该海域鱼类种类组成、多样性和群落结构及其与环境因子的关系进行了研究.结果表明: 该海域冬季捕获鱼类共60种,隶属于10目34科51属,以暖温性和暖水性底层鱼类为主.站位间物种丰富度指数介于1.14～2.84,多样性指数介于1.08～2.64,均匀度指数介于0.41～0.83之间.经聚类分析和非度量多维标度(MDS)分析,该海域鱼类群落在空间上可分为站位组Ⅰ(35° N以北水域站位)、站位组Ⅱ(靠近湾顶的近岸水域站位)和站位组Ⅲ(35° N以南水域站位).鱼类群落种类组成在站位组间及两两间的比较均差异极显著(R=0.45～0.91).典范对应分析表明,底层水温、水深和表层盐度是影响海州湾及邻近海域冬季鱼类群落结构的主要环境因子.     

Measuring community responses to large-scale disturbance in conservation biogeography

Aim   Which community metrics should be used to reflect community response to large-scale habitat alterations is unclear. Here, we assess what and how community changes should be measured to accurately track community responses to large-scale disturbance in space and/or time.
Location   France.
Method   We first developed a simulation model to examine temporal changes in the species composition of large-scale metacommunities. Using this model, we assessed how species richness, Shannon index, trends of particular subset of species or community indices of habitat specialization were influenced by different disturbance scenarios, and whether these indices were biased by imperfect detectability. We further used more than 1000 empirical bird communities from the French Breeding Bird Survey recently exposed to disturbances of various intensities as a case study.
Results   Our simulation and empirical results both demonstrate that species richness and diversity measures can show confusing trends and even provide misleading messages of communities' fate. In contrast, reflecting the composition of the community in terms of habitat specialist and generalist species was more robust and powerful to reflect disturbance effects.
Main conclusions   We highlight the weakness of using community metrics that fail to incorporate ecological difference among species when summarizing community-level trends in disturbed landscapes.