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This dataset presents the macrobenthic species abundance and biomass in soft bottom areas located at southeastern Bay of Biscay. Data on organic matter content and grain-size distribution in surficial seafloor sediments is also provided. Samples were obtained with Shipek and Smith-McIntyre type grabs in several surveys carried out between 2010 and 2020, covering a range of depths of 32–2241 m. Abundance and biomass of macrobenthic species are given. This database is useful for (i) research on spatial variability of macrobenthic communities, and (ii) baseline knowledge of species in the area. The research article on these data [1] was published in the journal Regional Studies in Marine Science. Title: Macrofaunal variability in the continental shelf and canyons in the southeastern Bay of Biscay.

Mobile fishing gears are responsible of various direct effects on benthic communities. The most important (in volume and value) fishery in Saudi waters of the Arabian Gulf is the 6-month trawl season for the green tiger shrimp. The fleet is composed of hundreds of artisanal boats carrying out short-duration tows of small trawls. To study the impact of this trawl season on local benthic communities, two different methodologies were adopted in three areas of different trawling intensities. The first study design was aimed at the seasonal effect and the second design examined the immediate impact after the pass of a trawl. Both studies were evaluated using univariate ecological indicators (richness, diversity, AMBI, M-AMBI) and the multivariate species composition. The seasonal study revealed a cyclic dynamics of the benthic assemblages. Most of the univariate ecological descriptors decreased during the trawling season and increased during the off-season while species composition undertook a round trip in multivariate space, thus supporting the conclusion that the impact of trawling on the benthic ecosystem during the shrimp season is reverted during the trawl ban. Although our results confirm predictions of synthetic statistical models, they also show that the impact of trawling on benthic communities strongly depend on the existence of a trawl ban period.

Monitoring and assessment of benthic communities have been routinely undertaken using morphology-based benthic indices, among which AZTI’s Marine Biotic Index (AMBI) and multivariate-AMBI (M-AMBI), are the most successful worldwide (Borja et al., 2019). They are used officially in routine monitoring in many European countries, where they have been intercalibrated (European Commission, 2018). AMBI has been mirrored by metabarcoding, and the genomic version (gAMBI; Aylagas et al., 2014) has demonstrated to yield results comparable to the morphological version. However, we have so far failed to develop a reliable genomic version of M-AMBI (M-gAMBI), which includes gAMBI, richness and diversity (Aylagas et al., 2018). This is because richness and diversity present very different results in morphological and genomic analyses. Since the multivariate method needs reference conditions, these must be set specifically for M-gAMBI to make its results comparable to those obtained with M-AMBI. To this aim, we started annual surveys in 2018, in 22 sampling locations, in Basque estuaries and coast. We present the results from the first three years of these surveys and discuss the problems faced when developing genomic reference conditions for M-gAMBI. The findings are of paramount importance for managers, since any new method or modification of an existing assessment method, needs to demonstrate that the results obtained when assessing the status are similar to those morphological-based methods, already approved and intercalibrated. Aylagas, E., Á. Borja, N. Rodríguez-Ezpeleta, 2014. Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI). PLoS ONE, 9: e90529. Aylagas, E., Á. Borja, I. Muxika, N. Rodríguez-Ezpeleta, 2018. Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks. Ecological Indicators, 95: 194-202. Borja, A., G. Chust, I. Muxika, 2019. Chapter Three - Forever young: The successful story of a marine biotic index. Advances in Marine Biology, 82: 93-127. European Commission, 2018. Commission Decision (EU) 2018/229 of 12 February 2018 establishing, pursuant to Directive 2000/60/EC of the European Parliament and of the Council, the values of the Member State monitoring system classifications as a result of the intercalibration exercise and repealing Commission Decision 2013/480/EU. Official Journal of the European Communities, L47: 1-91.

Global ocean warming, wave extreme events, and accelerating sea-level rise are challenges that coastal communities must address to anticipate damages in coming decades. The objective of this study is to undertake a time-series analysis of climate change (CC) indicators within the Bay of Biscay, including the Basque coast. We used an integrated and flexible methodology, based on Generalized Additive Mixed Models, to detect trends on 19 indicators (including marine physics, chemistry, atmosphere, hydrology, geomorphology, biodiversity, and commercial species). The results of 87 long-term time series analysed (~512,000 observations), in the last four decades, indicate four groups of climate regime shifts: 1) A gradual shift associated with CC starting in the 1980s, with a warming of the sea surface down to 100 m depth in the bay (0.10-0.25 °C per decade), increase in air temperature and insolation. This warming may have impacted on benthic community redistribution in the Basque coast, favouring warm-water species relative to cold-water species. Weight at age for anchovy and sardine decreased in the last two decades. 2) Deepening of the winter mixed layer depth in the south-eastern bay that probably led to increases in nutrients, surface oxygen, and chlorophyll concentration. Current increases on chlorophyll and zooplankton (i.e., copepods) biomass are contrary to those expected under CC scenarios in the region. 3) Sea-level rise (1.5-3.5 cm per decade since 1990s), associated with CC. 4) Increase of extreme wave height events of 16.8 cm per decade in the south-eastern bay, probably related to stormy conditions in the last decade, with impacts on beach erosion. Estimating accurate rates of sea warming, sea-level rise, extreme events, and foreseeing the future pathways of marine productivity, are key to define the best adaptation measures to minimize negative CC impacts in the region.

The use of genomic approaches to assist with biodiversity estimations is an alternative to traditional biomonitoring, which is very time-consuming and costly. In response to the high demand for quick community descriptions, DNA metabarcoding can simultaneously assign taxonomy to hundreds of samples rapidly and at low cost. However, the technique has not routinely been incorporated into biomonitoring network programs yet. Here, we applied DNA metabarcoding methodologies at stations within the monitoring network of the Basque Water Agency, the competent authority for the application of the European Water Framework Directive in this region. We characterized the benthic macroinvertebrate communities from 18 estuarine and coastal sediment samples using morphology and metabarcoding-based taxonomic identification and evaluated the performance of several versions of the AZTI’s Marine Biotic Index (AMBI). Although metabarcoding detected 112 taxa against the 206 taxa identified through morphology, we showed that metabarcoding leads to similar biomonitoring conclusions compared with traditional techniques. Using the abundance and biomass of those taxa detected from morphological methodologies, we found a significant positive correlation with the number of reads obtained with metabarcoding approaches. The metabarcoding-based index derived from read counts, gAMBI, and the morphology-based index derived from individuals’ biomass, (B)AMBI, showed the best correlation and revealed excellent agreement at determining the ecological status of the stations analyzed. We calculated that, for the analysis of the 51 stations included in the Basque monitoring network, metabarcoding was 55% less costly and 72% less time consuming. The results of our study are relevant to policy makers and researchers in the field of ecological assessment and will contribute to the quick implementation of DNA metabarcoding to intensive monitoring programs.

Marine renewable energy has considerable potential for enhancing the diversity of renewable sources, to reduce our reliance on fossil fuels and combat climate change. While the technological development of wave energy converters is progressing rapidly, their environmental impacts are still largely unknown, which is a barrier that could hinder their deployment. This research contributes to the state-of-the-art by introducing a framework for quantifying and analysing the ecological risks of three technologies (oscillating water columns, oscillating wave surge converters, and wave turbines). Based on a literature review, expert consultation process, and the development of a web tool, the potential pressures and the ecosystem elements that might be affected during the life cycle of a generic wave farm (an array of wave energy converters) are investigated. The main pressures are found to be physical disturbance, physical loss, hydrological change, and noise. The ecosystem elements sustaining the largest number of pressures and, therefore, at higher ecological risk are fish and cephalopods species, and benthic and pelagic habitats. The ecological risk assessment framework is operationalized into a free-access web tool ( https://aztidata.es/wec-era/ ) for the interactive assessment and visualisation of the pressures and ecological risks. The tool is intended to be used by managers, decision makers, scientists or promoters during the Strategic Environmental Assessment and Environmental Impact Assessment of wave energy projects. The novel approach presented in this work is more sophisticated than previous risk assessment matrices, enabling to better capture the complexity of the interactions between a wave farm and the environment.

The seafloor morphology of southeastern Bay of Biscay (Basque coast) consists of a narrow continental shelf and the Capbreton Canyon running almost parallel to the coastline and reaching up to 3060 m in depth. The south flank of the canyon is steep, and it is incised by northward trending canyons and gullies. Pockmark fields are observed in the interfluves of the tributary canyons. This heterogeneous morphology affects the regional oceanographic conditions, current patterns, and wave propagation, which influence the characteristics of pelagic and benthic habitats and their spatial distribution. This chapter describes the hard- and soft-bottom benthic communities at a depth of 100–927 m, occupying the main geomorphic features and habitats.

In 2000, the AZTI's Marine Biotic Index (AMBI) was published and was one of a number of marine benthic indices development to assess the ecological status of soft-bottom macroinvertebrates. This index, and its derivatives, has been very successful in its application to different geographical areas, across the world, as well as to different environments, from the intertidal to the abyssal, or from tidal freshwater to offshore habitats. In this review, we explain the story behind the AMBI development, and look for an explanation of the index's success. For doing that, we comment on the current practicalities of the index, we present the new AMBI species list, with 9251 taxa, we dismantle six myths around this index, and examine the past and the future of the index. We show that the solid ecological roots of the index make it a robust tool to assess the status of marine benthic communities, at any time and environment. Hence, we think that it will be 'forever young' helping managers in taking informed decisions to improve benthic marine systems.

To support ecosystem-based management and achieve the Good Environmental Status (GES) of marine waters it is important to better comprehend the relationships between biodiversity and environmental disturbance (anthropogenic and natural). Biotic indices are widely used in studies to help understanding these relationships and to assess the environmental status of waters. In recent years, trait-based indices rapidly emerged as an alternative ‘functional’ approach to serve this purpose. In this study, we analysed how two indices based upon the mean (community-weighted mean trait value–CWM) and the diversity of multiple traits (Rao’s quadratic entropy–Rao) in a macroinvertebrate community respond to natural- and anthropogenic seafloor disturbance (effluents) and we compared their performance with the widely used AMBI and M-AMBI. Our results demonstrate that CWM and Rao were not effective in indicating anthropogenic disturbance in the Basque coast, Bay of Biscay. The main reason was probably that many traits did not have a strong link with this type of disturbance. Besides, the mechanistic links between certain traits and their response to anthropogenic seafloor disturbance in marine environments is currently not well understood. From a management perspective: the CWM does not provide a single value indicating a quality status, which makes it a difficult tool to use and interpret. This index is probably more useful for scientists who want to explore and understand different aspects of community functioning. On the other hand, Rao and other indices expressing trait diversity do provide a single value of functioning; therefore they could potentially be effectively used for management purposes. However, to improve its performance, detailed and accurate trait data is required, which is currently lacking for many marine species.

In 2000, the AZTI's Marine Biotic Index (AMBI) was published and was one of a number of marine benthic indices development to assess the ecological status of soft-bottom macroinvertebrates. This index, and its derivatives, has been very successful in its application to different geographical areas, across the world, as well as to different environments, from the intertidal to the abyssal, or from tidal freshwater to offshore habitats. In this review, we explain the story behind the AMBI development, and look for an explanation of the index's success. For doing that, we comment on the current practicalities of the index, we present the new AMBI species list, with 9251 taxa, we dismantle six myths around this index, and examine the past and the future of the index. We show that the solid ecological roots of the index make it a robust tool to assess the status of marine benthic communities, at any time and environment. Hence, we think that it will be ‘forever young’ helping managers in taking informed decisions to improve benthic marine systems.

The sensitivity of the 15 indicators included in a complex aggregation method (Nested Environmental status Assessment Tool), applied to a case study in the Caspian Sea in Iran, has been studied to discriminate between areas impacted and non-impacted by bathing activities. Two methods were used: (i) the 15 indicators were grouped into four groups (physicochemical, bacteria, plankton, and benthos) and each group was investigated separately (one-way sensitivity analysis), calculating NEAT values after omitting each group independently; and (ii) indicators were selected randomly, using 1000 Monte Carlo iterations, and removing from 1 to 14 indicators at each iteration. The results revealed that the abundance of Pontogammarus was the single indicator that made the difference in assessing the status among locations, differentiating bathing and non-bathing areas. Hence, this indicator is regarded as a monitoring element detecting the impacts produced by a management measure (beach nourishment) taken by the authorities to maintain the bathing activity.

In recent decades, China has undergone an impressive development, which has produced increasing human pressures including coastal degradation. Bohai Bay, located in the west of the Bohai Sea (north of China), has been affected by various human pressures, including waste water discharges, land reclamation and oil exploitation. To monitor the effects of these pressures on this ecosystem, benthic macroinvertebrates and environmental variables (dissolved oxygen, nutrients, metals, etc.) were sampled in 2009 and 2011. To assess the ecological status of the benthic communities, the AZTI Marine Biotic Index (AMBI) and multivariate-AMBI (M-AMBI) were used, including both density and biomass in the calculation. This is the first research in which M-AMBI based on biomass (M-bAMBI) is applied. Both methods showed that the nearshore areas, especially close to the Haihe and Jiyun estuaries, were affected by human pressures, with a clear gradient of decreasing impacts offshore. The ecological status as assessed using density and biomass was quite similar. Significant relationships were also found between both methods and environmental variables. The use of AMBI and M-AMBI, based upon density and biomass, in assessing the ecological status of water bodies in China seems to be promising.

One of the main adaptation strategies to global change scenarios, aiming to preserve ecosystem functioning and biodiversity, is to maximise ecosystem resilience. The resilience of a species metapopulation can be improved by facilitating connectivity between local populations, which will prevent demographic stochasticity and inbreeding. The objective of this investigation is to estimate the degree of connectivity among estuarine species along the north-eastern Iberian coast, in order to assess community vulnerability to global change scenarios. To address this objective, two connectivity proxy types have been used based upon genetic and ecological drift processes: 1) DNA markers for the bivalve cockle (Cerastoderma edule) and seagrass Zostera noltei, and 2) the decrease in the number of species shared between two sites with geographic distance; neutral biodiversity theory predicts that dispersal limitation modulates this decrease, and this has been explored in estuarine plants and macroinvertebrates. Results indicate dispersal limitation for both saltmarsh plants and seagrass beds community and Z. noltei populations; this suggests they are especially vulnerable to expected climate changes on their habitats. In contrast, unstructured spatial pattern found in macroinvertebrate communities and in C. edule genetic populations in the area suggests that estuarine soft-bottom macroinvertebrates with planktonic larval dispersal strategies may have a high resilience capacity to moderate changes within their habitats. Our findings can help environmental managers to prioritise the most vulnerable species and habitats to be restored.

As the introduction of alien species represents one of the most important causes of biodiversity loss, it is crucial to study the distribution of alien species in order to control or eradicate their introduction and spread. Thus, the present study aimed to analyse the spatial distribution and temporal trends of soft-bottom marine benthic alien species collected during 20 years in the Nervion estuary, southeastern Bay of Biscay. Results indicated that, from a total of 6688 species records, 117 corresponded to alien species. Likewise, from a total of 742 different species identified, 23 species were classified as alien species. The two most frequently recorded alien species, Pseudopolydora paucibranchiata and Monocorophium acherusicum , appeared mainly at the intermediate part of the estuary that suffered historically an intense pollution. The presence and abundance of soft-bottom alien species became more evident since the mid-nineties, when the widening of the Bilbao Harbour occurred, together with a water quality improvement and the industry decline. Finally, although the identified alien species are considered as not invasive, the spread of alien species in the estuary might be considered as a threat.

The combined effects of human pressures (e.g., exploitation and wastewater discharges) and environmental variables (e.g., light, waves, temperature) have been studied only minimally in terms of sublittoral macroalgae resources. Using a long-term series (1993–2012) of cover and biomass of Gelidium corneum macroalgae, along the Basque coast (Bay of Biscay), the effects of human pressures and changes in climate have been studied. The biomass and the percentage of samples with p 5 m height. However, there are differences between sectors, with Gelidium biomass and cover being a function of the exploitation of this alga and wastewater discharges. In areas where these human pressures are present, the resource is more vulnerable to environmental changes, than in a sector in which human pressures are absent. Human pressures have reduced the resilience of these macroalgae beds, exacerbating the loss of biomass and macroalgae cover, under such climate changes. The implications of these findings, for the management of the resource in a sustainable way within the Water Framework Directive and the Marine Strategy Framework Directive, are discussed. There is a need for increasing resilience for macroalgae restoration along the Basque coast.

Using a long-term (1995–2014) monitoring network, from 51 sampling stations in estuaries and coasts of the Basque Country (Bay of Biscay), the objective of this investigation was to assess the responsiveness of 83 variables in water (18), sediments (27), biota (26), phytoplankton (2), macroinvertebrates (5) and fishes (5) to different human pressures and management actions. We used a total of 3247 series of data to analyse trends of improvement and worsening in quality. In a high percentage of the cases, the management actions taken have resulted in positive effects in the environment, as shown by the trend analysis in this investigation. Overall, much more trends of improvement than of worsening have been observed; this is true for almost all the media and biological components studied, with the exception of phytoplankton; and it applies as well to almost all the stations and water bodies, with the exception of those corresponding to areas with water treatment pending of accomplishment. In estuaries with decreasing human pressures during the period, the percentage of series showing quality improvement was higher (approx. 30%) than those showing worsening of quality (12%). Moreover, in those water bodies showing an increase of pressure, variables which can be considered indicators of anthropogenic effects showed negative trends (quality worsening). On the other hand, some of the variables analysed were more affected by natural variability than by changes in pressures. That was the case of silicate, nitrate and suspended solids, which followed trends correlated to salinity, which, in turn, was related to the rainfall regime during the study period.

Initially described in 2000, AZTI's Marine Biotic Index (AMBI) aims to assess alterations in communities of soft-bottom marine benthic macroinvertebrates caused by anthropogenic impacts. Although it was designed to be used in European estuaries and coasts this index, based on Pearson and Rosenberg's model of responses to organic enrichment, is being used successfully worldwide. Taking into account statistical difficulties associated with the use of raw abundance data, modifications to the index were recently proposed. These included transforming abundances prior to its calculation, or to use data other than abundances which might be more functionally relevant (such as biomass or production data). Using data from the Basque coast and estuaries (northern Spain), collected between 1995 and 2009, where the evolution of human pressures and restoration actions in the area may be taken into account, the performance of AMBI is compared to that of the proposed modifications in order to assess their usefulness. Despite large variations in the form and nature of the input data, all variations of AMBI index are shown to be highly correlated, even when presence/absence data are used. New boundaries between disturbance categories were calculated, reflecting inter-relationships between different forms of the index. The disturbance classification obtained from all variations using the recalculated boundaries agreed closely with that derived from AMBI. The finding that AMBI values calculated with presence/absence data are potentially useful opens up many possibilities, such as determining the status of assemblages retrospectively using historical data.

The aim of this paper is to develop a new methodology for assessing the quality of coastal waters along the Atlantic Iberian coasts, based upon Basque coast rocky intertidal assemblages, compliant with the European Water Framework Directive (WFD, 2000/60/EC). Biological data collected over a 20-year period, during the gradual introduction of a sewerage plan, are compared to several reference stations in order to differentiate various degrees of community alteration. A quality index (RICQI: Rocky Intertidal Community Quality Index) is drawn up, on the basis of: indicator species abundance; morphologically complex algae cover; species richness; and faunal cover (herbivore and suspensivore cover, proportion of fauna with respect to the whole assemblage). An independent dataset collected in Plentzia Bay (Basque coast, N. Spain), before and after the set-up of a wastewater treatment plant, is used in order to validate RICQI. A conceptual model based on our results is proposed, which describes successional stages of assemblages along a gradient of increasing environmental disturbance and associated values of the metrics included in the index. The performance of this new approach is compared with that of the quality of rocky bottoms index, used presently as the official method for assessing the ecological status of rocky assemblages in the Atlantic coastal waters of Spain. Both indices respond to changes in community structure, associated with pollution removal. However, the RICQI index shows a more accurate response, identifying different degrees of disturbance.

The impact of an off-shore fish farm in Alghero Bay (northwest Sardinia, Italy) on the benthic ecosystem was investigated in 2007 and 2008. In addition to studying the chemical and physical characteristics of the area (i.e., currents and sediment analyses), some biological analyses were also performed. The AZTI's Marine Biotic Index (AMBI) and the multivariate AMBI (M-AMBI) were calculated, which are being used in assessing the ecological status of benthic communities within the European Water Framework Directive (WFD). Clear impact gradients were detected according to both methods; they are related to farm production, prevailing currents, and characteristics of the area (i.e., water depth and distance to the cages). The site affected most was detected within 84 m from the cages; the area that no longer showed effects was over 907 m from the cages. The gradient is shown by decreasing AMBI values and percentage of opportunistic species and increasing richness, diversity, and the presence of sensitive species. This study highlights the importance of setting reference conditions for different areas when calculating M-AMBI. These reference conditions correspond to those in undisturbed sites in the opposite direction of the prevailing currents within the area.

The implementation of the Marine Strategy Framework Directive (MSFD) is directing European marine research towards the coordinated and integrated assessment of sea environmental status, following the ecosystem-based approach. The MSFD uses a set of 11 descriptors which, together, summarise the way in which the whole system functions. As such, the European Commission has proposed an extensive set of indicators, to assess environmental status. Hence, taking account of the large amount of data available for the Basque coast (southern Bay of Biscay), together with a recent proposal for assessment within the MSFD, an integrated environmental status assessment approach is developed (for the first time) in this contribution. The strengths and weaknesses of the method, combined with proposals from the MSFD, are discussed.

The European Water Framework Directive (WFD) requires monitoring programmes, to establish a coherent and comprehensive overview of ecological and chemical water status. Recently and within this context, the use of biomarkers has been proposed for incorporation into WFD monitoring programmes. In the present study, cages have been used to transplant (ranging between 14 and 75 days) adults of the dogwhelk Nassarius reticulatus in relation to a gradient of tributyltin (TBT) pollution; this is in order to evaluate its usefulness within the WFD monitoring programmes. Only the most polluted site (close to a shipyard) shows evidence of TBT contamination effects. As such, it may be concluded that the use of caged transplants with N. reticulatus (adults) is useful only for areas of high TBT pollution. Thus, within the European WFD context, this approach is generally not useful for surveillance and operational monitoring, but has some potential in investigative monitoring.

The European Union-funded ECASA project (Ecosystem Approach for Sustainable Aquaculture) studied the impacts from aquaculture on ecosystems from northern Norway to Greece. The objectives of this investigation were to identify quantitative indicators of the effects of aquaculture on marine communities, and to assess their applicability over a range of ecosystems and aquaculture production systems. The study included 6 Mediterranean and 4 Atlantic sites, 7 of which produced finfish (seabream, seabass, tuna, salmon and cod), and 2 bivalve molluscs (oysters, mussels, and clams); one site produced both fish and bivalves. Cultivation methods included finfish cages, long-lines and trestles. Similar sampling methodologies were employed at the 10 study sites, obtaining sediment, hydrodynamic, and benthic faunal data. The horizontal impact from organic enrichment extended 50 m from the farms, with contradictory responses in several indicators (individual abundance, biomass) and a more consistent response of the Infaunal Trophic Index (ITI) and AZTI's Marine Biotic Index (AMBI). By means of Partial Redundancy Analysis, it was demonstrated that the environmental variables explained 53.2% of the variability in the macrofaunal variables (individual abundance, species richness, diversity, AMBI and ITI), whilst the explained variance was partialled out within three groups of variables: (i) ‘hydrography’ (depth, distance to farm, average current speed), which explained 11.5% of the variance; (ii) ‘sediment’ (Eh and percentages of silt and total organic matter), which explained 5.4%; and (iii) ‘cages’ (years of production and annual production), which explained 15.2%. The shared variance explained by interactions among these groups was 21.1%. These results, together with multiple regression analysis, provide an accurate assessment of the degree of impact from aquaculture. In conclusion, the use of several benthic indicators, in assessing farm impacts, together with the investigation of dynamics of the studied location, water depth, years of farm activity, and total annual production, must be included when interpreting the response of benthic communities to organic enrichment from aquaculture.

The use of AMBI and M-AMBI in benthic quality assessments, within the European Water Framework Directive (WFD), has increased dramatically in recent years. M-AMBI is a multivariate tool, which incorporates AMBI, richness and Shannon diversity within the assessment. The response of this approach to different human pressures in coastal and estuarine waters has been investigated for the Basque Country (Northern Spain). In this contribution, several paradigmatic examples of these applications to different water bodies are presented. The time-series extend to samples collected between 1995 and 2007, showing the evolution of M-AMBI values under different pressures, i.e. urban and industrial discharges, dredging and disposal of sediments, and engineering works (such as land reclamation or marina construction), and, in addition, for illustrating the benthic quality recovery after positive actions have been undertaken, i.e. the removal of point-source discharges or water treatment programmes. In most cases, M-AMBI responds to these pressures as expected, with decreases in the ecological status immediately following the pressure. Conversely, when a pressure is removed, the recovery takes between 2 and 15 years, depending upon the intensity of the pressure and the characteristics of the water body. M-AMBI has been intercalibrated previously in coastal waters. After intercalibration in transitional waters, M-AMBI will be able to be used in the integrative quality assessment of European water bodies.

Levels of imposex (superimposition of male characters, upon females) and the presence of sterile females are assessed in the gastropod Nassarius reticulatus (L.), at 35 locations in the Basque Country. At 18 of these localities, organotin bioaccumulation (tributyltin (TBT); dibutyltin; monobutyltin) was evaluated, using isotope dilution GC–ICP–MS. Higher imposex levels and TBT body burden were found in confined harbours, with large vessel traffic or the presence of an offshore fleet. The highest values were found for the port of Pasaia, near to a shipyard (a relative penis size index of up to 92%, and TBT body burden up to 405 ng g−1 – given on a dry weight basis as Sn). Imposex effects were evaluated also in parasitized females, at some of the sampling sites. The percentage of presence of c-type Vas Deferens sequence stages (i.e., with vas deferens beginning at the oviduct opening) was higher in parasitized females. In turn, there was an absence of highly convoluted oviduct in parasitized females.

The European Water Framework and Marine Strategy Directives relate to the assessment of ecological quality, within estuarine and coastal systems. This legislation requires quality to be defined in an integrative way, using several biological elements (phytoplankton, benthos, algae, phanerogams, and fishes), together with physico-chemical elements (including pollutants). This contribution describes a methodology that integrates all of this information into a unique quality assessment for 51 stations from 18 water bodies, within the Basque Country. These water bodies are distributed into four typologies, including soft-bottom coastal areas and three types of estuaries. For each station, decision trees were used to integrate (i) water, sediment and biomonitor chemical data to achieve an integrated physico-chemical assessment and (ii) multiple biological ecosystem elements into an integrated biological assessment. Depending on the availability of ecological quality ratios or global quality values, different integration schemes were used to combine station assessments into water body assessments on a single scale. Several examples from each element have been selected, to illustrate their responses to different pressures; likewise, to establish how the assessed integrated quality has changed, over time. The results made biological and ecological sense and physico-chemical improvements were often correlated with improvements in the quality of benthos and fishes. These tools permit policy makers and managers to take decisions, based upon scientific knowledge, in water management, regarding the mitigation of human pressures and associated recovery processes.

Legislation in US and Europe has been adopted to determine the ecological integrity of estuarine and coastal waters, including, as one of the most relevant elements, the benthic macroinvertebrate communities. It has been recommended that greater emphasis should be placed on evaluating the suitability of existing indices prior to developing new ones. This study compares two widely used measures of ecological integrity, the Benthic Index of Biotic Integrity (B-IBI) developed in USA and the European AZTI's Marine Biotic Index (AMBI) and its multivariate extension, the M-AMBI. Specific objectives were to identify the frequency, magnitude, and nature of differences in assessment of Chesapeake Bay sites as ‘degraded’ or ‘undegraded’ by the indices. A dataset of 275 subtidal samples taken in 2003 from Chesapeake Bay were used in this comparison. Linear regression of B-IBI and AMBI, accounted for 24% of the variability; however, when evaluated by salinity regimes, the explained variability increased in polyhaline (38%), high mesohaline (38%), and low mesohaline (35%) habitats, remained similar in the tidal freshwater (25%), and decreased in oligohaline areas (17%). Using the M-AMBI, the explained variability increased to 43% for linear regression, and 54% for logarithmic regression. By salinity regime, the highest explained variability was found in high mesohaline and low polyhaline areas (53–63%), while the lowest explained variability was in the oligohaline and tidal freshwater areas (6–17%). The total disagreement between methods, in terms of degraded-undegraded classifications, was 28%, with high spatial levels of agreement. Our study suggests that different methodologies in assessing benthic quality can provide similar results even though these methods have been developed within different geographical areas.

Since AMBI was published originally in 2000, it has been used in an increasing number of investigations with monitoring purposes, or to analyse impacts on soft-bottom macrobenthic communities. Some guidelines for its correct use were published in 2005; however, a main issue remained without an answer — which are the minimal area and number of replicates necessary, to obtain a precise estimate for AMBI? In this study, new methodologies such as bootstrap techniques have been applied to this particular problem. Data were obtained from sampling carried out in 1995, within the framework of the Littoral Water Quality Monitoring and Control Network of the Basque Country (northern Spain). The sampling strategy consisted of 11 intertidal estuarine sampling stations (0.25m2, sampled for each of six replicates) and 17 subtidal estuarine and coastal sampling stations (0.125m2, sampled for each of six replicates). Two replicates have been established as being sufficient, both for intertidal and subtidal sampling stations, to classify 80% of the pseudosamples into the same disturbance level, in terms of AMBI, for 64% of the stations. For the minimal area, it has been determined also (for both intertidal and subtidal sampling stations) that 0.25m2 is sufficient to classify 80% of the iterations into the same disturbance level, for 64% of the stations.

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 European Water Framework Directive (WFD) establishes a framework for the protection and improvement of transitional and coastal waters; its final objective is to achieve at least 'good water status' for all waters, by 2015. The WFD requires Member States (MSs) to assess the Ecological Status (ES) of water bodies. This assessment will be based upon the status of the biological, hydromorphological and physico-chemical quality elements, by comparing data obtained from monitoring networks to reference (undisturbed) conditions, and then deriving an Ecological Quality Ratio (EQR). One of the biological quality elements to be considered is the benthic invertebrate component and some structural parameters (composition, diversity and disturbance-sensitive taxa) must be included in the ES assessment. Following these criteria, several approaches to benthic invertebrate assessment have been proposed by MSs. The WFD requires that these approaches are intercalibrated. This contribution describes the comparison of the different methodologies proposed by United Kingdom, Spain, Denmark and Norway. Results show a high consistency between the approaches, both with regard to determining the EQR and boundary settings for the ES.

Although a plethora of benthic indices exist, there is no agreement on what index or indices should be used by environmental managers to establish benthic quality. The objective of this investigation was to rank 35 benthic quality assessment indices used in different countries to evaluate the impact produced by 15 different human pressures (including multipressure, aquaculture, sewage discharges, eutrophication, physical alteration, chemical pollution, climate change, etc.). The ranking was determined by taking into account the coverage area of biogeographical provinces, number of citations testing a pressure and number of citations with significant correlation with pressure. We analysed 363 references, of which 169 showed quantitative data. Over a potential total score of 100, the highest values were obtained by the following indices: (i) AZTI’s Marine Biotic Index (AMBI), which scored 77, tested by using 14 pressures in 14 provinces from the Arctic to tropical seas; (ii) multivariate AMBI (M-AMBI), which scored 74, tested with 12 pressures in 13 provinces; (iii) Bentix (BENTIX), which scored 68, tested with nine pressures in six provinces; (iv) Benthic Quality Index (BQI), which scored 66, tested with five pressures in seven provinces; and (v) Benthic Opportunistic Polychaetes Amphipods (BOPA) index, which scored 62, tested with eight pressures in six provinces.

The monitoring of marine benthic communities is based upon their ability to integrate long-term environmental conditions and it is considered an efficient, accurate and useful tool in the detection of pollution effects. However, long-term studies are scarce, and only few are devoted to recovery processes in estuaries following water treatment. In this contribution, the response of the Nervion estuary to sewerage processes is studied, using a long-term (1989 to 2003) data set of physico-chemical (dissolved oxygen, redox potential, organic matter, metals) and biological (density, richness and diversity in benthic communities) variables. The AMBI (AZTI's Marine Biotic Index) was designed to investigate the response of soft-bottom communities to natural and human-induced changes in European coastal water quality and is evaluated here. The first factor controlling the Nervion's benthic structure is found to be the bottom water oxygen saturation, hypoxia- and/or anoxia-produced azoic sediments. When water treatment commenced, benthic recolonisation was very rapid in terms of opportunistic species settlement. However, the community structure was highly disturbed, in terms of density, richness, diversity and AMBI values. AMBI and diversity values are highly correlated with oxygen saturation. When the water treatment continued, the high metal con- centrations in the sediments inhibited recovery in some areas; they were a secondary factor in deter- mining benthic structure. This contribution demonstrates that the AMBI is an efficient tool for detect- ing changes in benthic communities and in systems associated with sewerage schemes; it provides an indication of the proportions of opportunistic and sensitive species within a long-term series.

The European Water Framework Directive (WFD) establishes a framework for the protection of groundwater, inland surface waters, estuarine waters, and coastal waters. The WFD constitutes a new view of water resources management in Europe, based mainly upon ecological elements; its final objective is achieving at least ‘good ecological quality status’ for all water bodies by 2015. The approach to identify these water bodies includes, amongst others, the sub-division of a water body into smaller water bodies, according to pressures and resulting impacts. The analyses of pressures and impacts must consider how pressures would be likely to develop, prior to 2015, in ways that would place water bodies at risk of failing to achieve ecological good status, if appropriate programmes of measures were not designed and implemented. This contribution focuses on the use of the DPSIR (Driver, Pressure, State, Impact, Response) approach, in assessing the pressures and risk of failing the abovementioned objective, using the Basque (northern Spain) estuarine and coastal waters as a case study, using the following steps: (i) determination of the water bodies to be analysed; (ii) identification and description of the driving forces producing pressures over the region; (iii) identification of all existing pressures within the water bodies; (iv) identification, from them, of the most relevant pressures; (v) determination, from the relevant pressures, of those which are significant; (vi) assessing the impacts on water bodies (in terms of ecological and chemical impacts); and (vii) assessing the risk of failing the WFD objectives.

Marine protected areas play an important role in the conservation of marine resources and fisheries management. In the Basque Country (northern Spain), the small (158 ha) Gaztelugatxe Marine Reserve was established in 1998; after 5 years without exploitation, it is considered likely that the goose barnacle Pollicipes pollicipes populations have recovered. This contribution provides information on the standing stock, and of the relationships between biomass, coverage, and density, and environmental factors such as wave height and energy derived from waves received at the coast. Increasing energy levels produce enhanced coverage and abundance, providing a bigger standing stock in the reserve. Numerical models to simulate the energy produced by waves can be used as a tool to predict the potential biomass of the goose barnacle along the coast. Such an approach allows comparison of observed and predicted biomasses, and possibly also determination of the factors involved in the observed differences, e.g. overexploitation and pollution; this will assist in assessing goose barnacle resources along the coast.

In recent years, several benthic biotic indices have been proposed to be used as ecological indicators in estuarine and coastal waters. One such indicator, the AZTI Marine Biotic Index (AMBI), was designed to establish the ecological quality of European coasts. The index examined the response of soft-bottom benthic communities to natural and man-induced disturbances in coastal and estuarine environments. It has been successfully applied to different geographical areas and under different impact sources, with increasing user numbers in European marine waters (Baltic, North Sea, Atlantic and Mediterranean). The AMBI has been used also for the determination of the ecological quality status (EcoQ) within the context of the European Water Framework Directive (WFD). In this contribution, 38 different applications including six new case studies (hypoxia processes, sand extraction, oil platform impacts, engineering works, dredging and fish aquaculture) are presented. The results show the response of the benthic communities to different disturbance sources in a simple way. Those communities act as ecological indicators of the ‘health’ of the system, indicating clearly the gradient associated with the disturbance. # 2004 Elsevier Ltd. All rights reserved.

Following the European Water Framework Directive (2000/60/EC), the authors proposed, in a previous contribution, a Marine Biotic Coefficient (BC) to establish the ecological quality of soft-bottom benthos within European estuarine and coastal environments. The present study examines the application of the BC to the Atlantic (North Sea; Bay of Biscay; South of Spain) and Mediterranean (Spain and Greece) European coasts. The investigation assesses also the usefulness of the BC, in relation to different impact sources (e.g. drilling cuts with ester-based mud, submarine outfalls, heavy metals, industrial and mining wastes, jetties and sewerage works). The results obtained are consistent with those obtained using several methods and parameters, such as richness, diversity, evenness, Abundance–Biomass comparison plots and univariate and multivariate statistical analyses. The BC values provide a simple and clearly defined way to establish the ecological quality of soft-bottom benthos, complementary to the above mentioned methods.

The effects of pollutants on marine fauna and flora cover many direct and indirect effects at supraindividual levels, from populations to ecosystems. In recent times, hundreds of indicators, metrics, and assessment methods have been developed to determine the impacts of those pollutants on different components of the ecosystem. This development is generally included in the framework of national and international legislation, approved in different continents. Pollution effects on organisms can imply consequences at the population level to different degrees, from changes in population dynamics or genetic diversity, to the local extinction of a population. In turn, ecological integrity assessment requires the study of structure (e.g., richness, diversity), function (e.g., response of sensitive and opportunistic species or biological traits to pollution), and processes at the community level. However, the most important challenge is to understand the response of the complete ecosystem to interactions between multiple stressors (i.e., cumulative, synergistic, antagonistic) and to assess marine health in an integrative way at regional or global scales.