A review of approaches for classifying benthic habitats and evaluating habitat quality

Long-term trends in benthic habitat quality as determined by Multivariate AMBI and Infaunal Quality Index in relation to natural variability: a case study in Kinsale Harbour, south coast of Ireland

Benthic Ecological Quality Ratios (EQR) are important tools for assessing the ecological status of coastal and transitional water bodies. Here, we use spatial and time-series data from Kinsale Harbour, Ireland to examine the effects of sample processing methodologies on the outputs of two EQRs: Multivariate AMBI (M-AMBI) and Infaunal Quality Index (IQI). Both EQRs were robust to changes in sieve size from 1mm to 0.5mm, and to changes in the taxa identified in spatial calibration. Both EQRs classified habitat quality in Kinsale as generally Good or High with no evidence of significant change over the time series (1981-2006). IQI classified the ecological status as higher than M-AMBI. There was a significant relationship between IQI and M-AMBI in spatial calibration, but no significant relationship between them in time series. Further research into the behaviour of EQRs in relation to natural variability over long time-scales is needed to discriminate anthropogenic impacts reliably.

Response of single benthic metrics and multi-metric methods to anthropogenic pressure gradients, in five distinct European coastal and transitional ecosystems

In recent times many benthic indices have been proposed to assess the ecological quality of marine waters worldwide. In this study we compared single metrics and multi-metric methods to assess coastal and transitional benthic status along human pressure gradients in five distinct environments across Europe: Varna bay and lake (Bulgaria), Lesina lagoon (Italy), Mondego estuary (Portugal), Basque coast (Spain) and Oslofjord (Norway). Hence, 13 single metrics (abundance, number of taxa, and several diversity and sensitivity indices) and eight of the most common indices used within the European Water Framework Directive (WFD) for benthic assessment were selected: index of size spectra (ISS), Benthic assessment tool (BAT), Norwegian quality index (NQI), Multivariate AMBI (M-AMBI), Benthic quality index (BQI), (Benthic ecosystem quality index (BEQI), Benthic index based on taxonomic sufficiency (BITS), and infaunal quality index (IQI). Within each system, sampling sites were ordered in an increasing pressure gradient according to a preliminary classification based on professional judgement. The different indices are largely consistent in their response to pressure gradient, except in some particular cases (i.e. BITS, in all cases, or ISS when a low number of individuals is present). Inconsistencies between indicator responses were most pronounced in transitional waters (i.e. IQI, BEQI), highlighting the difficulties of the generic application of indicators to all marine, estuarine and lagoonal environments. However, some of the single (i.e. ecological groups approach, diversity, richness) and multi-metric methods (i.e. BAT, M-AMBI, NQI) were able to detect such gradients both in transitional and coastal environments, being these multi-metric methods more consistent in the detection than single indices. This study highlights the importance of survey design and good reference conditions for some indicators. The agreement observed between different methodologies and their ability to detect quality trends across distinct environments constitutes a promising result for the implementation of the WFD's monitoring plans. Moreover, these results have management implications, regarding the dangers of misclassification, uncertainty in the assessment, use of conflicting indices, and testing and validation of indices.

The use of benthic indicators in Europe: from the Water Framework Directive to the Marine Strategy Framework Directive

The Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD) are the European umbrella regulations for water systems. It is a challenge for the scientific community to translate the principles of these directives into realistic and accurate approaches. The aim of this paper, conducted by the Benthos Ecology Working Group of ICES, is to describe how the principles have been translated, which were the challenges and best way forward. We have tackled the following principles: the ecosystem-based approach, the development of benthic indicators, the definition of 'pristine' or sustainable conditions, the detection of pressures and the development of monitoring programs. We concluded that testing and integrating the different approaches was facilitated during the WFD process, which led to further insights and improvements, which the MSFD can rely upon. Expert involvement in the entire implementation process proved to be of vital importance.

Ecological Quality Status of the soft-bottom communities on the Algerian coast: general patterns and diagnosis

Between 1995 and 2001, the soft-bottom communities along the 1180 km of the Algerian coast were sampled in nine gulfs and 12 harbours, providing a total of 655 samples. Eight macrozoobenthos-based biotic indices (S, N, H', BQI, AMBI, BENTIX, BO2A and ITI) were selected to describe the general patterns of the coastal water quality status and to establish a quality diagnosis for the different zones subjected to anthropogenic pressure (e.g., harbour construction, industrial and urban pollution). Reference values were determined for each of the eight indices selected by analyzing the indices' parameter distribution. The Ecological Quality Ratio (EQR) was estimated for each index, resulting in an EQR Mean Score and an EQR Bad Score. From these EQR, we defined an EQS for each sample. The agreement between these EQS was analysed using the Kappa method in order to propose a survey strategy for the Algerian coastal waters that would take into account the soft-bottom biological compartment. The results clearly indicate that high and good quality assessments are prevalent in the gulfs, while quality assessments in harbours vary greatly from bad to good. The effect of pollution observed in the harbours can be classified in two main groups, according to when they were constructed and their relative degree of openness to the sea, which permits better water circulation and probably dilutes the pollution.

Environmental quality of Korean coasts as determined by modified Shannon-Wiener evenness proportion

The coast of the Korean peninsula experiences a range of human impacts, including pollution, shipping, reclamation, and aquaculture, that have motivated numerous local studies of macrobenthic organisms. In this paper, 1,492 subtidal stations were compiled from 23 studies (areas) to evaluate environmental quality on a broader scale. A common index in biomonitoring, Shannon-Wiener evenness proportion (SEP), could not incorporate azoic or single-species samples. This shortcoming was overcome by developing an inverse function of SEP (ISEP), which was positively correlated with independent measures of water quality available for nine sites and was not biased by the size of the sampling unit. Additionally, at Shihwa Dike, where samples were collected before and after reinstating a tidal connection with the ocean, ISEP values improved over time, as expected. Thus, it is now possible to assign Korean subtidal sites to seven ISEP "grades" and to use their values and trends to guide coastal management.

Carbon and nitrogen stable isotopes in coastal benthic populations under multiple organic enrichment sources

In a dispersive coastal area under multiple organic enrichment sources, stable isotopes were used to trace organic sources of carbon and nitrogen in sediments and benthic macrofauna. The Bivalve Abra alba and the Polychaetes Nephtys sp. and Pectinaria (Lagis) koreni were reliable indicators of the input of terrestrial-derived organic matter into this coastal area, either originated in outfall sewage discharges or estuarine outflow. An isotopic depletion was observed up to 250 m from the outfall branches, much stronger in the biota than in the sediments. An enrichment of 2 ‰ in the sediments, and 2-6 ‰ in the species was noticed in sites located farther than 1500 m from the outfall. Depositivores and carnivores/omnivores gave the best picture of the extension of the sewage dispersion and incorporation into the food web.

Benthic indicators: From subjectivity to objectivity - Where is the line?

Over the last few years, the interest in using benthic indicators to assess marine environments has increased dramatically after a rather long period of relative stagnation, mostly due to the need to assess the status of coastal marine waters required by North American and European regulations. Numerous papers on this topic have been published in the domain of ecology, using a variety of different terms to refer to two categories of information: benthic species and the status of benthic communities. Nowadays, the abundant literature on these two categories makes it possible to comment on (1) the definition of the different terms used by benthic researchers, (2) the current increase of papers of rising complexity about benthic indicators, and (3) the subjectivity and objectivity involved in using benthic indicators. Faced with the increase in the number of methods, we recommend pragmatism and thus the transfer of simple methods to the research consultancies that are responsible for assessing benthic quality in numerous impact studies. Using certain procedures, such as the "sentinel species", the best professional judgement (BPJ) and taxonomic sufficiency (TS), should clearly be encouraged.

Assessing coastal benthic macrofauna community condition using best professional judgement--developing consensus across North America and Europe

Benthic indices are typically developed independently by habitat, making their incorporation into large geographic scale assessments potentially problematic because of scaling inequities. A potential solution is to establish common scaling using expert best professional judgment (BPJ). To test if experts from different geographies agree on condition assessment, sixteen experts from four regions in USA and Europe were provided species-abundance data for twelve sites per region. They ranked samples from best to worst condition and classified samples into four condition (quality) categories. Site rankings were highly correlated among experts, regardless of whether they were assessing samples from their home region. There was also good agreement on condition category, though agreement was better for samples at extremes of the disturbance gradient. The absence of regional bias suggests that expert judgment is a viable means for establishing a uniform scale to calibrate indices consistently across geographic regions.

Exploring the marine biotic index (AMBI): variations on a theme by Angel Borja

The results of manipulating the input data to AMBI are explored using various transformations of numerical species abundance (NAMBI), biomass (BAMBI) and production (PAMBI) from a variety of stations on the NE Atlantic shelf at which the pollution/disturbance status is known. There is a close agreement between the proportions of species in the five AMBI ecological groups and a phylum level meta-analysis axis of increasing environmental impact. All AMBI measures provide a better monotonic relationship with the impact axis than do traditional species diversity measures, which show higher diversity at intermediate levels of disturbance. A marginally better relationship with the impact axis of the meta-analysis is achieved by a moderate (square root) transformation of the data. 'Production' data (an appropriate combination of abundance and biomass information) provide only a marginal improvement on abundance data, but are ecologically and functionally much more relevant. Severe transformation of the data, culminating in presence/absence, degrades the relationship with the impact axis, but if only simple species lists are available then these may still be useable in making an environmental assessment.

Marine habitat classification for ecosystem-based management: a proposed hierarchical framework

Creating a habitat classification and mapping system for marine and coastal ecosystems is a daunting challenge due to the complex array of habitats that shift on various spatial and temporal scales. To meet this challenge, several countries have, or are developing, national classification systems and mapping protocols for marine habitats. To be effectively applied by scientists and managers it is essential that classification systems be comprehensive and incorporate pertinent physical, geological, biological, and anthropogenic habitat characteristics. Current systems tend to provide over-simplified conceptual structures that do not capture biological habitat complexity, marginalize anthropogenic features, and remain largely untested at finer scales. We propose a multi-scale hierarchical framework with a particular focus on finer scale habitat classification levels and conceptual schematics to guide habitat studies and management decisions. A case study using published data is included to compare the proposed framework with existing schemes. The example demonstrates how the proposed framework's inclusion of user-defined variables, a combined top-down and bottom-up approach, and multi-scale hierarchical organization can facilitate examination of marine habitats and inform management decisions.

Ecological quality assessment of the lower Lima Estuary

Monitoring biotic factors is gaining in importance within Europe, due in large extent to the ecological approach of the European Water Framework Directive (WFD) and the importance attributed to biological elements in the assessment of quality status. Despite its ecological importance, the Lima Estuary is subjected to a range of perturbations, including urban, agricultural and industrial waste discharge, dredging activities, and introduction of non-indigenous invasive species. This work uses macrozoobenthic data to study the ecological status of the lower Lima Estuary where most disturbance factors are concentrated. We were able to verify consistent differences along space, and to identify different degrees of disturbance in the estuarine area. These results allow us to suggest cost-effective approaches to monitor this estuarine area, aiming on contributing to effective management actions.

Influence of macrofauna long-term natural variability on benthic indices used in ecological quality assessment

An essential prerequisite for the assessment of the ecological quality of marine ecosystems is the understanding of the natural variability and its effect on the performance of quality indices. This study is focused on the long-term natural variability of diversity, biotic and multimetric indices by using long-term macrofauna data of a coastal area in the southern North Sea (1978-2005). The univariate and most biotic and multimetric indices respond significantly on specific natural disturbance events such as cold winters, but the strength of response varied between indices as well as between events. As a result, the ecological quality status can decrease over a range of 3 (out of 5) classification units. The overall ecological quality was good to high, but an increase of indices occurred from the mid 1980s onwards due to changes in the climate regime. This long-term variability has to be considered within ecological quality assessment schemes.

Assessment of marine benthic quality change in gradients of disturbance: comparison of different Scandinavian multi-metric indices

Three multi-metric benthic macrofauna indices were used to assess marine benthic ecological quality status (EcoQS) according to the European Water Framework Directive, in seven pollution gradients mainly, western Scandinavia. The impacts included organic load, hypoxia, metals, urban effluents and physical disturbance. The indices responded in a similar threshold fashion, irrespective of impact factor identity. Usually, the border between Good and Moderate EcoQS (G/M), is determined as some deviation from a reference situation. References, however, are difficult to find. An alternative procedure is described to estimate the G/M border, not requiring reference data. Thresholds, where faunal structure deterioration commences, were identified from non-linear regressions between indices and impact factors. Index values from the less impacted side of the thresholds were assumed to come from environments of Good and High EcoQS, and the 5th percentile of these data, was defined as the G/M border. Estimated G/M borders compared well with previous studies.

Theoretical and practical aspects on benthic quality assessment according to the EU-Water Framework Directive--examples from Swedish waters

A previously presented objective method to calculate each species sensitivity to disturbance is here slightly modified and implemented in the Benthic Quality Index (BQI) for marine benthic invertebrates. A framework for assessment of water bodies based on multi-site BQI-values is also presented, where a certain variation of BQI-values is allowed to cover the heterogeneity within each water body. The 20th percentile, using bootstrapping, from the available sites' BQI-values is compared with the status boundaries for quality assessment. The reliability of the assessment depends on the background information available for the boundary setting as well as the number of sampling sites included in the assessment. Agreement between time series of quality assessments in areas with known changes in anthropogenic disturbances is encouraging. Problems associated with water body assessment based on few or no samples, as well as multiple sampling occasions during the 6-yr WFD cycle are discussed.

The robustness of ecological indicators to detect long-term changes in the macrobenthos of estuarine systems

Accurate and reliable benthic quality indicators are in great demand following the recent developments and the strict time schedule for implementing the European Water Framework Directive. The Mondego estuary has experienced a progressive deterioration during the 1990s, followed by a partial ecological recovery due to restoration measures in 1997/1998. We have used the estuary as a model system to test the performance and robustness of a set of ecological indicators in highlighting the changes in the ecological state of intertidal areas. Over a period of 17 years (1985-2002), we calculated Margalef, Shannon-Wiener, Berger-Parker, Taxonomic Distinctness measures, AZTI's Marine Biotic Index, Infaunal Trophic Index, and Eco-Exergy based indices and tested differences across periods characterised by different anthropogenic disturbance. We combined temporal data within three periods: before, during and after disturbance, based on progressive information on the changes in the extended type of anthropogenic disturbance. Indices were then compared with biological and abiotic descriptors (macroalgae, macrophytes, benthic macrofauna, nutrients concentration, sediment grain size and total organic carbon). We found great disparity in the indicators ability to capture temporal changes, showing distinct performances at each site. At the Zostera noltii site, only Margalef, Total Taxonomic Distinctness and the thermodynamically based indices captured temporal changes, despite giving higher values during the disturbance period. At the bare sediment site, Taxonomic Distinctness, ITI, Shannon-Wiener, Berger-Parker, AMBI and the TBI were able to distinguish between periods, in agreement with the differences observed analysing the macrobenthic assemblages. Furthermore, Taxonomic Distinctness was not robust enough to detect any temporal or spatial change. We thus suggest further research to understand the behaviour of ecological indicators, in view of their crucial importance for the management and protection of marine coastal areas.

Applying Benthic Index of Biotic Integrity in a soft bottom ecosystem in North of the Persian Gulf

In this study, the Chesapeake Bay Benthic Index of Biotic Integrity (B-IBI) was selected in an attempt to describe ecological health of soft bottom channels (Khowr-e Musa) in North of the Persian Gulf. Most of study area was found to be in degraded or severely degraded conditions. B-IBI scores were ranged between 1 and 3.86. Comparison ofmacrobenthos abundance and organic content between two developmental periods showed significant difference (p < 0.05). After the establishment and development of petrochemical industries, the abundance of macrofauna decreased (809 to 239 individuals m(-2)) and organic content increased leading to organic enrichment (15.3 to 22.4%). Three new sources of organic matter were found to be important namely industrial waste, sewage and mangrove litter. After 1999 about 6 millions Avicennia marina tree were planted near petrochemical zone in the area. Study area changed rapidly in the last decade and region is under severely anthropogenic impacts. The present study showed that Khowr-e Musa is under both natural stress and anthropogenic impacts and two main impacts could be attributed to the organic enrichment and to the dredging. Choice of suitable management plans and metric controls could help to the salvage of the largest tidal channel complex in Persian Gulf.

Medium-term assessment of the effects of the Prestige oil spill on estuarine benthic communities in Cantabria (Northern Spain, Bay of Biscay)

A specific monitoring program was implemented in the estuaries of Cantabria (northern Spain) in order to assess the medium-term effects (2003-2005) of the Prestige oil spill (POS) on benthic macroinvertebrate communities. A control-impact design was adopted, examining four unaffected and five oil-affected estuaries. High mortalities and significant differences in overall richness and diversity between the control and impacted estuaries were not detected. Some changes in the temporal evolution of species abundance were observed for some key species, but these could not be related to the spillage event. It was not possible to ensure that low magnitude effects had not occurred, due to the high range of natural variability of benthic communities, the confounding effects of other contamination sources and the absence of previous reference conditions.

Assessing benthic community condition in Chesapeake Bay: does the use of different benthic indices matter?

Federal and state environmental agencies conduct several programs to characterize the environmental condition of Chesapeake Bay. These programs use different benthic indices and survey designs, and have produced assessments that differ in the estimate of the extent of benthic community degradation in Chesapeake Bay. Provided that the survey designs are unbiased, differences may exist in the ability of these indices to identify environmental degradation. In this study we compared the results of three indices calculated on the same data, and the assessments of two programs: the Chesapeake Bay Program and the Mid-Atlantic Integrated Assessment (MAIA). We examined the level of agreement of index results using site-based measures of agreement, evaluated sampling designs and statistical estimation methods, and tested for significant differences in assessments. Comparison of ratings of individual sites was done within separate categories of water and sediment quality to identify which indices summarize best pollution problems in Chesapeake Bay. The use of different benthic indices by these programs produced assessments that differed significantly in the estimate of degradation. A larger fraction of poor sites was classified as good by the Environmental Monitoring and Assessment Program's Virginian Province and MAIA benthic indices compared to the Chesapeake Bay benthic index of biotic integrity, although overall classification efficiencies were similar for all indices. Differences in survey design also contributed to differences in assessments. The relative difference between the indices remained the same when they were applied to an independent dataset, suggesting that the indices can be calibrated to produce consistent results.

Calibration and evaluation of five indicators of benthic community condition in two California bay and estuary habitats

Many types of indices have been developed to assess benthic invertebrate community condition, but there have been few studies evaluating the relative performance of different index approaches. Here we calibrate and compare the performance of five indices: the Benthic Response Index (BRI), Benthic Quality Index (BQI), Relative Benthic Index (RBI), River Invertebrate Prediction and Classification System (RIVPACS), and the Index of Biotic Integrity (IBI). We also examine whether index performance improves when the different indices, which rely on measurement of different properties, are used in combination. The five indices were calibrated for two geographies using 238 samples from southern California marine bays and 125 samples from polyhaline San Francisco Bay. Index performance was evaluated by comparing index assessments of 35 sites to the best professional judgment of nine benthic experts. None of the individual indices performed as well as the average expert in ranking sample condition or evaluating whether benthic assemblages exhibited evidence of disturbance. However, several index combinations outperformed the average expert. When results from both habitats were combined, two four-index combinations and a three-index combination performed best. However, performance differences among several combinations were small enough that factors such as logistics can also become a consideration in index selection.

Assessing ecological integrity in marine waters, using multiple indices and ecosystem components: challenges for the future

During the last decade, there have been substantial scientific advances in the development of indices that measure the condition of biological ecosystem elements in coastal and estuarine waters. Though successful, these advances were only the initial steps and a special session on use of indices in ecological integrity assessments was held at the Coastal and Estuarine Research Federation meeting to focus the field on the most appropriate directions for the next decade. The session identified four primary scientific challenges: (i) reduce the array of indices by identifying the index approaches that are most widely successful; (ii) establish minimum criteria for index validation; (iii) intercalibrate methods to achieve uniform assessment scales across geographies and habitats; and (iv) integrate indices across ecosystem elements. Where an explosion of indices characterized the last decade, the next decade needs to be characterized by consolidation. With increased knowledge and understanding about the strengths and weaknesses of competing index approaches, the field needs to unify approaches that provide managers with the simple answers they need to use ecological condition information effectively and efficiently.

Ocean fertilization: a potential means of geoengineering?

The oceans sequester carbon from the atmosphere partly as a result of biological productivity. Over much of the ocean surface, this productivity is limited by essential nutrients and we discuss whether it is likely that sequestration can be enhanced by supplying limiting nutrients. Various methods of supply have been suggested and we discuss the efficacy of each and the potential side effects that may develop as a result. Our conclusion is that these methods have the potential to enhance sequestration but that the current level of knowledge from the observations and modelling carried out to date does not provide a sound foundation on which to make clear predictions or recommendations. For ocean fertilization to become a viable option to sequester CO2, we need more extensive and targeted fieldwork and better mathematical models of ocean biogeochemical processes. Models are needed both to interpret field observations and to make reliable predictions about the side effects of large-scale fertilization. They would also be an essential tool with which to verify that sequestration has effectively taken place. There is considerable urgency to address climate change mitigation and this demands that new fieldwork plans are developed rapidly. In contrast to previous experiments, these must focus on the specific objective which is to assess the possibilities of CO2 sequestration through fertilization.

Assessing estuarine environmental quality using fish-based indices: performance evaluation under climatic instability

The seasonal variation of five selected multimetric indices for the determination of the Ecological Quality Status (EQS) of transitional waters was evaluated, as well as the indices' responses to an extreme drought event that occurred in 2005. The database used regards the Mondego River estuary, which was sampled from June 2003 to August 2006 on a monthly basis. Among the selected indices (EBI-Deegan et al. [Deegan, L., Finn, J.T., Ayvazlan, S.G., Ryder-Kieffer, C.A., Buonaccoesi, J., 1997. Development and validation of an Estuarine Biotic Integrity Index. Estuaries 30(3), 601-617], EDI-Borja et al. [Borja, A., Franco, J., Valencia, V., Bald, J., Muxika, I., Belzunce, M.J., Solaun, O., 2004. Implementation of the European Water Framework Directive from the Basque Country (northern Spain): a methodological approach. Marine Pollution Bulletin 48(3-4), 209-218], EFCI-Harrison and Whitfield [Harrison, T.D., Whitfield, A.K., 2004. A multi-metric fish index to assess the environmental condition of estuaries. Journal of Fish Biology 65, 683-710], EBI-Breine et al. [Breine, J.J., Maes, J., Quataert, P., Van den Bergh, E., Simoens, I., Van Thuyne, G., Belpaire, C., 2007. A fish-based assessment tool for the ecological quality of the brackish Scheldt estuary in Flanders (Belgium). Hydrobiologia 575, 141-159] and TFCI - Coates et al. [Coates, S., Waugh, A., Anwar, A., Robson, M., 2007. Efficacy of a multi-metric fish index as an analysis tool for the transitional fish component of the Water Framework Directive. Marine Pollution Bulletin 55, 225-240]), the EBI by Breine et al. (2007) was the only that evidenced clear interannual and seasonal variations. The EQS by the several indices ranged from "Low" to "High", depending on the index considered, evidencing the high level of mismatch between indices. The results are discussed in the scope of the EU Water Framework Directive, regarding monitoring strategies, application of indices and EQS assessment.

Is it possible to assess the ecological status of highly stressed natural estuarine environments using macroinvertebrates indices?

Several biotic indices have been proposed for the assessment of the ecological status of benthic macroinvertebrates in marine waters, although none have been generally accepted. When it comes to assessing highly stressed natural environments, such as estuaries, the controversy and uncertainty is much higher than for any given normal index. In this article, we test the behavior and suitability of different biotic indices proposed under the perspective of the Water Framework Directive (S, H, AMBI, M-AMBI, BQI, W-statistic, Taxonomic distinctness) for the assessment of estuaries in northern Spain. The low species richness and dominance of a few tolerant species in the characteristic community of these estuaries presented a challenge to the application of the biotic indices tested. Combined approaches that integrate different aspects of water quality and ecosystem functionality could increase the reliability of the ecological assessment of these transitional waters.

Development of a fish-based multimetric index to assess the ecological quality of marine habitats: the Marine Fish Community Index

In this paper the Marine Fish Community Index (MFCI) for the assessment of ecological status of marine environment is proposed. The MFCI was divided into 4 typologies: Rocky subtidal; shallow, intermediate and deep soft-bottoms. Based on the typical community associated to each typology and the DPSIR analysis performed, a set of metrics were selected and tested through a multiple correlation matrix (Pearson's coefficient) and the core ones included in the index. The MFCI was applied in all typologies and the scores obtained with each metric were analyzed. In order to test the robustness of the MFCI the final ecological value of each zone was recalculated by removing successively one metric at a time. The MFCI showed a sensitive and robust response in the ecological status assessment. Since it incorporates both functional and structural community information, the MFCI can be useful in the context of the Marine Strategy Framework Directive as well as in other contexts of conservation and sustainable management of the marine environment.

Efficacy of adapted estuarine fish-based multimetric indices as tools for evaluating ecological status of the marine environment

The assessment of ecological status of marine fish communities required by the marine strategy framework directive (MSFD) emphasises the need for fish-based ecological indices in marine waters. In this study we adapt five estuarine multimetric indices to the marine environment and apply them in three types of substrates, analysing the metrics responsible for the obtained patterns of ecological status. The results show inefficiency of the community degradation index (CDI) and the biological health index (BHI) in ecological status assessment and disagreement between the estuarine biotic integrity index (EBI), the estuarine fish community index (EFCI) and the transitional fish classification index (TFCI). Analysis of individual metrics suggests lack of representativeness and consideration for the particularities of each substrate's typical fish communities. None of the tested indices were efficient on the marine environment, urging the need for new marine indices that account for differences between types of substrate and depth.

Investigating habitat value to inform contaminant remediation options: approach

Habitat valuation methods are most often developed and used to prioritize candidate lands for conservation. In this study the intent of habitat valuation was to inform the decision-making process for remediation of chemical contaminants on specific lands or surface water bodies. Methods were developed to summarize dimensions of habitat value for six representative aquatic and terrestrial contaminated sites at the East Tennessee Technology Park (ETTP) on the US Department of Energy Oak Ridge Reservation in Oak Ridge, TN, USA. Several general valuation metrics were developed for three broad categories: site use by groups of organisms, site rarity, and use value added from spatial context. Examples of use value metrics are taxa richness, a direct measure of number of species that inhabit an area, complexity of habitat structure, an indirect measure of potential number of species that may use the area, and land use designation, a measure of the length of time that the area will be available for use. Measures of rarity included presence of rare species or communities. Examples of metrics for habitat use value added from spatial context included similarity or complementarity of neighboring habitat patches and presence of habitat corridors. More specific metrics were developed for groups of organisms in contaminated streams, ponds, and terrestrial ecosystems. For each of these metrics, cutoff values for high, medium, and low habitat value were suggested, based on available information on distributions of organisms and landscape features, as well as habitat use information. A companion paper describes the implementation of these habitat valuation metrics and scoring criteria in the remedial investigation for ETTP.

Overview of integrative tools and methods in assessing ecological integrity in estuarine and coastal systems worldwide

In recent years, several sets of legislation worldwide (Oceans Act in USA, Australia or Canada; Water Framework Directive or Marine Strategy in Europe, National Water Act in South Africa, etc.) have been developed in order to address ecological quality or integrity, within estuarine and coastal systems. Most such legislation seeks to define quality in an integrative way, by using several biological elements, together with physico-chemical and pollution elements. Such an approach allows assessment of ecological status at the ecosystem level ('ecosystem approach' or 'holistic approach' methodologies), rather than at species level (e.g. mussel biomonitoring or Mussel Watch) or just at chemical level (i.e. quality objectives) alone. Increasing attention has been paid to the development of tools for different physico-chemical or biological (phytoplankton, zooplankton, benthos, algae, phanerogams, fishes) elements of the ecosystems. However, few methodologies integrate all the elements into a single evaluation of a water body. The need for such integrative tools to assess ecosystem quality is very important, both from a scientific and stakeholder point of view. Politicians and managers need information from simple and pragmatic, but scientifically sound methodologies, in order to show to society the evolution of a zone (estuary, coastal area, etc.), taking into account human pressures or recovery processes. These approaches include: (i) multidisciplinarity, inherent in the teams involved in their implementation; (ii) integration of biotic and abiotic factors; (iii) accurate and validated methods in determining ecological integrity; and (iv) adequate indicators to follow the evolution of the monitored ecosystems. While some countries increasingly use the establishment of marine parks to conserve marine biodiversity and ecological integrity, there is awareness (e.g. in Australia) that conservation and management of marine ecosystems cannot be restricted to Marine Protected Areas but must include areas outside such reserves. This contribution reviews the current situation of integrative ecological assessment worldwide, by presenting several examples from each of the continents: Africa, Asia, Australia, Europe and North America.

Ecological status assessment in the lower Eo estuary (Spain). The challenge of habitat heterogeneity integration: a benthic perspective

The implementation of the European Water Framework Directive (WFD) requires evaluation of the ecological status (ES) of benthic communities in coastal and transitional water systems, and the intercalibration of assessment methodologies therefore becomes a research challenge. Our aim was to test the suitability of applying the M-AMBI index to assess the status of the Eo estuary (northern coast of Spain). Our results showed that M-AMBI was influenced by the natural variability of benthic communities, and presented an apparent dependence on habitat characteristics. Consequently, the definition of homogeneous areas in transitional water systems should be based on the salinity gradient combined with other factors. To achieve an accurate ES assessment, habitat-specific reference conditions should then be defined prior to the application of M-AMBI; this necessitates dividing an estuary into several sections, which may be classified as different ESs. From this perspective, a novel approach to integrate habitat heterogeneity in a global ES assessment was tested.

Use of multimetric indices to classify estuaries with different hydromorphological characteristics and different levels of human pressure

The assessment of estuaries based on benthic communities is widely used to determine impacts caused by human pressure and is one of the required tools for the implementation of the European Water Framework Directive (WFD). Our study compared multimetric approaches (B-IBI and TICOR) to assess the benthic condition of three Portuguese estuaries (Mondego, Tejo, and Mira rivers) with different levels of natural and human induced stress. Benthic community condition was classified into quality status categories of the WFD and compared for consistency with a priori status categories based upon physical-chemical criteria. Both multimetric indices discriminated equally well between locations classified above or below the good status category but were unable to provide good separation between other quality classes (high/good, moderate, poor/bad). Metrics included in these indices are greatly affected by natural stress and we recommend the development of habitat-specific thresholds to increase the discriminatory ability of any benthic condition index.

Towards a classification of organic enrichment in marine sediments based on biogeochemical indicators

A nomogram is developed to show that pH, redox potentials (Eh(NHE)) and measures of dissolved sulfides (H2S + HS(-) + S(2-))(total free S(2-)) can be used to classify organic enrichment impacts in marine sediments. The biogeochemical cycle of sulfur in marine sediments is described to show that changes in macrobenthic infauna community structure associated with high levels of organic matter supply result from stress due to oxygen deficiency (hypoxia and anoxia) and toxic effects of S(2-). The changes reflect enhancement of microbial sulfate reduction under conditions of high organic matter sedimentation and the progressive formation of hypoxic-anoxic conditions measured by decreased Eh NHE and increased concentrations of S(2-). The nomogram provides a basis for classification of the oxic status of marine sediments based on changes in inter-related biological and biogeochemical variables along an organic enrichment gradient.

Distribution and ecological relevance of fine sediments in organic-enriched lagoons: the case study of the Cabras lagoon (Sardinia, Italy)

In organic-enriched sedimentary systems, like many Mediterranean coastal lagoons, a detailed analysis of sediment grain size composition and partitioning within the muds is crucial to investigate sedimentological trends related to both hydrodynamic energy and basin morphology. In these systems, sediment dynamics are particularly important because the partitioning and transport of fine sediments can strongly influence the redistribution and accumulation of large amounts of organic matter, and consequently the distribution of benthic assemblages and the trophic status and functioning of a lagoon. Nevertheless, studies on benthic-sediment relationships have been based mainly on a rather coarse analysis of sediment grain size features. In muddy systems, however, this approach may impede a proper evaluation of the relationships and effects of the distribution of fine sediment and organic matter on the biotic benthic components. Here we show that the distribution of sedimentary organic matter (OM) and total organic carbon (TOC) in the Cabras lagoon (Sardinia, Italy) can be explained (i.e., predicted) as a function of a nonlinear increase in the amount of the cohesive fraction of sediments (< or = 8 microm grain size particles) and that this fraction strongly influences the structure, composition and distribution of macrobenthic assemblages. Even in such a homogeneously muddy system, characterized by "naturally" occurring impoverished communities, impaired benthic assemblages were found at < or = 8 microm, OM, TOC contents of about 77%, 11% and 3.5%, respectively. A review of studies conducted in Mediterranean coastal lagoons highlighted a lack of direct integrated analysis of sediment features and the biotic components. We suggest that, especially in organic-enriched coastal lagoons, monitoring programs should primarily investigate and consider the cohesive fraction of sediments in order to allow a better assessment of benthic-sediment relationships and ecological quality of the system.

A report card and quality indicators for the Seine estuary: from scientific approach to operational tool

The scientific teams from the interdisciplinary Seine-Aval (SA) research program and the SA's operational pole, GIPSA (Groupement d'Intérêt Public Seine-Aval) have worked together to create a report card designed to help the Estuary Council (Conseil de l'Estuaire) revitalize its original functions: maintaining functional links between the various estuarine ecosystems, comprehending and managing the estuary's natural habitats and biological populations, and monitoring and improving the physical-chemical quality of the estuarine waters. The report card will be able to synthesize the information obtained from several system performance variables and available operational indicators. This approach, intended to guide the estuary managers, is the oeuvre of several scientific teams; it is particularly important in the context of the Water Framework Directive because it facilitates the elaboration of a group of relevant indicators, which can then be used as operational tools. A report card will provide decision-makers (e.g., political authorities; national, regional and local institutions and industries) with the key indicators for evaluating the system and predicting changes in terms of selected objectives, such as the preservation and restoration of the estuary's environmental functionalities. The final objective of the research is to choose among the available indicators to approximate potential ecological risks. Integrating the socio-economical data will perhaps lead to setting risk acceptability thresholds for the different uses of the Seine estuary. In the end, collaboration between the scientists, the managers, and the GIPSA operational pole will be essential to produce a viable report card about the environmental status of the Seine estuary. To illustrate the research now under way, this article presents the results for three actions undertaken, concerning: (i) physical indicators (i.e., an inventory of the estuary first as a whole, and then section by section); (ii) benthic indicators (i.e., seven indices which show a moderate EcoQ for the lower part of the estuary); and (iii) a eutrophication indicator (i.e., an indicator for coastal eutrophication potential (ICEP), which helps to limit the nutrient fluxes (N or P) that exceed the silica flux delivered by the Seine network, based on the Redfield ratios for algal propagation).

Evaluation of the applicability of a fuzzy index of ecosystem integrity (FINE) to characterize the status of Tyrrhenian lagoons

The new index FINE, a multimetric, fuzzy-based index for the evaluation of environmental quality for Mediterranean transitional waters, was calculated using biotic data gathered between 2000 and 2006 at 15 stations in 4 Tyrrhenian transitional water ecosystems (Orbetello Lagoon, Padrongiano Delta, Stagno di S. Teodoro, and Stagno di Tortolì), i.e. in a different biogeographic sub-province respect to the one in which the index was developed and validated. The rationale of FINE is that certain attributes, selected on the basis of established principles of benthic ecology, are fundamental for lagoon ecosystem function. A set of other indices (Simpson's 1-lambda', the W-statistics, AMBI, and BOPA) was also calculated and compared to FINE outputs. FINE, 1-lambda', and the W-statistics were significantly correlated with sedimentary organic matter content. Some stations were unequivocally assigned to the same ecological status, independently from the index used; for others, some discrepancies were evident. Mediterranean transitional waters probably share ecosystem complexities which are not yet fully captured by indices developed and validated elsewhere.

Influence of seasonal variability in benthic invertebrate community structure on the use of biotic indices to assess the ecological status of a Portuguese estuary

The present study focused on the use of benthic invertebrate communities to assess the ecological quality of a Portuguese estuary characterized by strong seasonal changes and with eutrophication problems. Seasonal benthic samples were collected during a flood year and the methodology proposed by the WFD Portuguese group was used to classify benthic assemblages into five different quality classes. Factor analysis was applied to classify stations based on their physical-chemical status. Different classifications were obtained with different indices and among seasons and there was low agreement between indices and index-season interactions. Diversity indices were better correlated to eutrophication related variables than AMBI and ABC method. Predictable responses of benthic indices to anthropogenic stress symptoms were stronger during the dry period.

Zoobenthos as indicators of ecological status in coastal brackish waters: a comparative study from the Baltic Sea

A new method for classifying soft-bottom zoobenthic assemblages along the Finnish coasts (northern Baltic Sea) is presented and tested against traditional physicochemical monitoring data in the complex Archipelago Sea. Although multivariate methods for assessing the state of the marine environment have become widely used, few numerical indices can operate over a wide salinity range. We compare indices currently in use and propose a new index, BBI (brackish water benthic index), for the low-saline and species-poor Baltic coastal waters. BBI offers a salinity-corrected tool for classification of the soft-bottom zoobenthos under the demands of the European Union Water Framework Directive.

Polychaete/amphipod ratio revisited

In this paper, we reexamine the opportunistic polychaete/amphipod ratio, modifying it to allow estuarine and coastal communities to be divided into the five classes suggested by the European Water Framework Directive (WFD). The resulting biological index, called the BOPA index, considers the total number of individuals collected in the samples, the frequency of opportunistic polychaetes, and the frequency of amphipods (except the genus Jassa). After comparing this new index to AMBI and BENTIX, two other indices that have been proposed in the literature, we tested it in two situations involving soft-bottom communities in the English Channel (Bay of Morlaix and Bay of Seine). Our results show that the BOPA index is simple to use. Amphipods and opportunistic polychaetes (21 species, nine genus and two families from the AZTI list for a total of 3459 taxa) are easy to identify, providing that both the number of these organisms in a sample and the total number of individuals collected (independent of the sampling surface) is known. The BOPA is appropriate for use in the poorest communities whose total number of individuals exceeds 20 individuals.

Paradox of estuarine quality: benthic indicators and indices, consensus or debate for the future

The European Water Framework Directive will have instituted the concept of Ecological Quality Status (EQS) as a way to assess the biological quality of water masses. The EQS will be based mainly upon the composition of the different biological compartments in the ecosystem specially the benthos as compared to certain reference sites. Such management tools are already well established for freshwater (i.e. biotic indices), but not for coastal and estuarine (i.e. transitional) waters. In the framework of the Seine-Aval programme a workshop on benthic indicators was organized at Wimereux (France) in June 2005. The aim of this workshop and this paper is (1) to present the experiences of the Seine Aval researchers, and the French scientific approaches to benthic indicators, with those international experiences and approaches that have been published or are under development; and (2) to examine the existing benthic tools and their possible use in the characterization of the state of estuarine ecosystems. The debate during the workshop and the numerous recently published on the WFD are discussed in term of the implementation of the WFD in transitional water bodies using benthic indicators and indices. Some proposals for the future underline the needs to re-examine and adapt the different index thresholds, to take into account physical disturbances, to inventory the existing conditions vs reference conditions and to be as pragmatic as possible in using the WFD in transitional waters.

Using historical data, expert judgement and multivariate analysis in assessing reference conditions and benthic ecological status, according to the European Water Framework Directive

The European Water Framework Directive (WFD) establishes a framework for the protection and improvement of estuarine and coastal waters, trying to achieve 'good surface water status at the latest 15 years after the date of entry into force of this Directive'. One of the biological elements that should be analysed is the benthos and, as such, the WFD normative definitions describe the aspects of the benthic communities that must be included in the ecological status assessment of a water body. Therefore, it is essential to include, in the assessment, the different metrics that address those parameters identified in the normative definitions for each of the ecological status classes. In this contribution the use of the AMBI, richness and diversity, combined with the use, in a further development, of factor analysis together with discriminant analysis, is presented as an objective tool (named here M-AMBI) in assessing ecological quality status. This assessment requires previous classification of water bodies and typologies, together with the definition of reference conditions; this is undertaken in this contribution using historical data, expert judgement and multivariate analysis. The study has been undertaken by examining changes in benthic communities in the Basque Country, over the last decade, as a case-study, to demonstrate the accuracy and potential of these methodologies.

The ecological quality status of the Bay of Seine and the Seine estuary: use of biotic indices

Using recent indices developed, in part, for use under the European Water Framework Directive (AMBI, BENTIX, BOPA, BQI, I2EC and the trophic index ITI), the ecological quality status of two highly contaminated environments--the Bay of Seine and the Seine estuary (Eastern English Channel)--was determined on several spatial and temporal scales. Data from 604 observations gathered over a 14-year period (1988-2002) were analyzed, and the results used to show the relationship between biotic indices, environmental variables and classic descriptors (e.g., number of species, total abundance, dominance index, ES(50) and Shannon/Brillouin diversities). Though the specific ecological quality (EcoQ) values calculated with the various indices were different, the overall trend of the results was similar. Synthesizing the values produced by the six indices used in the study allowed attribution of a high to good EcoQ status to the Bay of Seine and a moderate EcoQ to the estuary. The mesh size used when processing samples was proved to have no effect in winter on the EcoQ values for either body of water.

European environmental management: moving to an ecosystem approach

The European Union has adopted several environmental directives, strategies, recommendations, and agreements that require a shift from local- or regional-based regulations to more ecosystem-based, holistic environmental management. Over the next decade, environmental management in Europe is likely to focus more on biological and ecological conditions rather than physical and chemical conditions, with ecosystem health at the center of regulation and management decision making. Successful implementation of this new ecosystem management and strategic assessment process in Europe will require the integration of regulatory and technical information and extensive collaboration from among European Union member countries, between agencies, and across disciplines to an unprecedented degree. It will also require extensive efforts to adapt current systems of environmental assessment and management to the basin and ecosystem level, across media and habitats, and considering a much broader set of impacts on ecosystem status than is currently addressed in most risk assessments. This will require the understanding, integration, and communication of economic, ecological, hydrological, and other processes across many spatial and temporal scales. This article discusses these challenges and describes some of the research initiatives that will help achieve integrated ecosystem management in Europe.

Characterization of the ecological quality of the coastal Gulf of Lions (NW Mediterranean). A comparative approach based on three biotic indices

The ecological quality of the Gulf of Lions coast was assessed using three biotic indices (H', AMBI and BQI). The three indices correlated positively. The positive correlation between AMBI and BQI was surprising and was mostly due to the fact that the dominant species Ditrupa arietina featured a low ES50(0.05) but was classified in GI by AMBI. Both H' and BQI were efficient in distinguishing impacted from un-impacted sites but AMBI was not. Differences between H' and BQI were mainly due to the scale used to translate indices in terms of EcoQ. The three indices were able to detect the major changes in macrofauna composition, which occurred in the Bay of Banyuls-sur-Mer during the last 40years. However, the interpretations of such changes in terms of EcoQ differed between indices. These results are discussed relative to the characteristics of the tested indices.

Monitoring transitional waters using reduced benthic assemblages

In this study, the use of reduced assemblages of benthic invertebrate taxa is proposed to describe similarity relationships between samples from transitional environments. A data set from four different studies, made up of 641 samples for a total 203 species, was analysed using permutation randomisation tests in order to extract a pool of taxa able to approximate the full set of species. The identified "operational set", comprising 19 taxa, was capable of adequately reproduce similarity relationships between samples (Rho>0.90, p<0.001). All selected taxa were easily extractable from the samples and easy identifiable by non-specialised technicians; these characteristics were considered appropriate for the development of rapid and cost-effective monitoring procedures based on benthic invertebrate assemblages.