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

Influence of hydraulic clam dredging and seasonal environmental changes on macro-benthic communities in the Southern Adriatic (Central Mediterranean Sea)

Macro-benthic communities on the shallowest soft bottoms are impacted by hydraulic dredgers used for the harvesting of the striped venus clam (Chamelea gallina). Changes in macro-benthic assemblages were analysed across four areas in the Southern Adriatic Sea (Central Mediterranean Sea) during the winter and summer 2022 (low and high fishing pressures, respectively). Two sampling surveys were carried out collecting abundance data (N/100m2) of 69 species. Diversity indices (Shannon-Weiner and Equitability) were calculated and differences between seasons and areas were tested using non-parametric tests. Changes in the assemblage and feeding habits were explored by adopting permutational multivariate analysis of variance on 34 species. Moreover, environmental conditions of all areas in the two seasons were characterized by a set of 8 variables. Seasonal changes in diversity were only detected for the Shannon-Weiner index, with values significantly higher in winter than summer. Macro-benthic assemblages differed between the two seasons, and the winter assemblages were well-distinct in each area. In contrast, a high overlap was shown in the summer assemblages of the four areas. Changes in feeding habits showed an increase in filter feeding polychaetes and opportunistic/scavenger species during the summer. Temperature, Salinity and primary production were positively correlated to summer stations indicating potential thermic stress on the assemblages. The results provide information on the benthic community impacted by dredge disturbance and seasonal changes driven by environmental conditions, stressing the need to integrate these aspects in assessments on the health status of marine ecosystems required by European directives and fishery management plans.

Pollution status determination using trace metals and organic contaminants of the water column in coastal areas of the Red Sea and the Gulf of Aqaba: A baseline assessment

Herein, we aim to provide a baseline assessment of the pollution status of the water column in coastal areas of Saudi Arabia (Red Sea and the Gulf of Aqaba), using trace metals (Cd, Co, Cr, Cu, Ni, Pb and Zn), total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs), in seawater samples obtained from 71 sampling stations in June-July 2021. Concerning trace metals, the maximum concentrations for Co, Cu and Ni were detected in Al-Shuqaiq, whereas the highest Pb and Zn concentrations were found in the Jeddah lagoon waters. Elevated concentrations of TPHs and the highest sum of PAHs were recorded in surface waters of Al Lith, Jeddah lagoon and Jeddah Mena. Overall, the concentrations of all trace metals, TPHs and individual PAHs for which environmental standards have been stipulated for the Kingdom of Saudi Arabia fall well below the threshold values.

A multi-metric fish index to measure the ecological quality of tropical predominantly open estuaries along the western coast of India

Defining the ecological quality of estuaries is challenging because of the inadequacy of available methods and indices to characterise the ecosystem. In Indian estuaries, there are no scientific attempts to establish multi-metric fish index to determine the ecological status. A multi-metric fish index (EMFI) was customised for twelve predominantly open estuaries on India's western coast. The index was established at the individual estuary level to ensure uniformity and contrast from sixteen metrics that designate the fish community and diversity, composition and abundance, estuarine use and trophic integrity from 2016 to 2019. A sensitivity study was followed to measure the responses of the EMFI under different metric varying scenarios. There were seven metrics identified as the most prominent for the EMFI in metric alteration scenarios. We also deduced a composite pressure index (CPI) based on the anthropogenic pressures described for the estuaries. The ecological quality ratios (EQR) defined based on EMFI (EQR_E) and the CPI (EQR_P) for all the estuaries were positively correlated. The EQR_E values calculated based on the regression relationship (EQR_E on EQR_P) showed the divisions from 0.43 (bad) to 0.71 (high) for the Indian west coast estuaries. Similarly, the standardised CPI (EQR_P) values for different estuaries indicated that the values range from 0.37 to 0.61. Our results based on the EMFI suggest four estuarine systems (33%) as 'good', seven (58%) as 'moderate' and one (9%) as 'poor'. Generalised Linear Mixed Model for EQR_E showed that EQR_P and estuary influenced EQR_E; however, the effect of year was not significant. This comprehensive study based on the EMFI is the first record for predominantly open estuaries along the Indian coast. Therefore, the EMFI established in this study could be reliably advocated as a sound, effective and composite tool of ecological quality for tropical open transitional waters.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Ecological quality status assessment of tropical estuaries with benthic indices using differently derived reference conditions

Setting appropriate reference conditions (RCs) is critical for classifying the Ecological Quality Status (EcoQS) which is extremely challenging, considering the present-day estuaries. The EcoQS of three tropical estuaries was assessed by applying five different RCs to identify the best applicable method for the area. The AZTI's indices (AMBI and M-AMBI) categorised areas with sharper pollution gradient with ease, while classification of moderate-low polluted areas was ambiguous. Indices responded to chemical stressors more clearly in the impacted estuary compared to the less polluted estuaries. Ecological status assigned by the default RC (lowest AMBI and highest diversity and richness values) were more accurate than those obtained on application of other four types of RCs, owing to various estuarine constraints that are discussed herewith. Thus, prior to application, caution should be exercised while setting area-specific RCs. The inclusion of combination of AZTI's indices with professional judgment for successful appraisal of ecosystem is recommended.

Simple Is the Best: An Alternative Method for the Analysis of Free-Living Nematode Assemblage Structure

An alternative approach to notice changes of the nematode community structure was evaluated in five study cases in the Mediterranean Sea. In detail, we suggested a combination of morpho-functional traits (i.e., amphid, cuticle, buccal cavity, and tail shape) as an alternative to the taxonomic identification of nematodes. The results clearly demonstrated that the matrixes made using the trait code numbers perfectly mirror the changes of the nematode community structure at the genus level. The combination of the morpho-functional traits more frequently observed in areas under human pressure were ascribable to genera belonging to Xyalidae, Linhomoeidae and Chromadoridae families. This approach might greatly speed the analyses of nematode fauna in biomonitoring programs and might also be adopted for other meiobenthic organisms that may be categorized in functional groups opening new perspectives in the ecological assessment of meiofauna.

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

One key component of any eutrophication management strategy is establishment of realistic thresholds above which negative impacts become significant and provision of ecosystem services is threatened. This paper introduces a toolkit of statistical approaches with which such thresholds can be set, explaining their rationale and situations under which each is effective. All methods assume a causal relationship between nutrients and biota, but we also recognise that nutrients rarely act in isolation. Many of the simpler methods have limited applicability when other stressors are present. Where relationships between nutrients and biota are strong, regression is recommended. Regression relationships can be extended to include additional stressors or variables responsible for variation between water bodies. However, when the relationship between nutrients and biota is weaker, categorical approaches are recommended. Of these, binomial regression and an approach based on classification mismatch are most effective although both will underestimate threshold concentrations if a second stressor is present. Whilst approaches such as changepoint analysis are not particularly useful for meeting the specific needs of EU legislation, other multivariate approaches (e.g. decision trees) may have a role to play. When other stressors are present quantile regression allows thresholds to be established which set limits above which nutrients are likely to influence the biota, irrespective of other pressures. The statistical methods in the toolkit may be useful as part of a management strategy, but more sophisticated approaches, often generating thresholds appropriate to individual water bodies rather than to broadly defined "types", are likely to be necessary too. The importance of understanding underlying ecological processes as well as correct selection and application of methods is emphasised, along with the need to consider local regulatory and decision-making systems, and the ease with which outcomes can be communicated to non-technical audiences.

Eco-assessment of least disturbed areas of the Antalya River basin: application of diatom indices from different ecoregions

Biomonitoring of least disturbed areas is a crucial issue to accurately assess the ecological status of surface waters and ensure their sustainability. Diatom metrics are important tools for the assessment of environmental conditions of lotic ecosystems to achieve environmental sustainability. The present study was aimed to evaluate the ecological status of least disturbed areas in the Antalya River basin (Turkey) using diatom indices developed from different ecoregion. Diatom species such as Cymbella excisa, Achnanthidium minutissimum, Cocconeis euglypta, and Cocconeis placentula were the most contributing species to the dissimilarity of sampling stations between rainy and dry seasons. The first two axes of canonical correspondence analysis (CCA) elucidated a strong (86%) correlation between diatom taxa and stressors. Results of the Monte Carlo permutation test indicated that total phosphorus (TP), water temperature, Tin (Sn), total organic carbon, zinc, and pH are significantly influential ecological factors on the distribution of diatom taxa among sampling stations. The Spearman correlation rank test indicated that diatom indices had significant positive and negative correlations with TP gradient. Results revealed that diatom indices developed from different ecoregions have different scores for the eco-assessment of similar sampling stations. European diatom indices mostly showed similar behavior in the bioassessment of the ecological status of rivers in the Antalya region compared to the different ecoregion. Among European diatom indices, TIT was more competitive and could give better results in the bio-evaluation of rivers in the Antalya River basin. Using diatom indices developed from different ecoregions may lead to an erroneous assessment of water quality. Accordingly, ecoregional specific diatom metrics are needed to accurately determine the surface water quality. Eco-assessment of least disturbed areas of the Antalya River basin: application of diatom indices from different ecoregions: Abuzer Çelekli, Ömer Lekesiz, Tolga Çetin.

Long-term response of marine benthic fauna to thin-layer capping with powdered activated carbon in the Grenland fjords, Norway

The Grenland fjords in Norway have a long history of contamination by large emissions of dioxins and mercury. As a possible sediment remediation method in situ, thin-layer capping with powdered activated carbon (AC) mixed with clay was applied at two test sites at 30 m and 95 m depth in the Grenland fjords. This study presents long-term effects of the AC treatment on the benthic community structure, i.e. nine years after capping. Capping with AC significantly reduced the number of species, their abundance and biomass at the two test sites, compared to uncapped reference sites. At the more shallow site, the dominant brittle star species Amphiura filiformis disappeared shortly after capping and did not re-establish nine years after capping. At the deeper site, the AC treatment also caused long-lasting negative effects on the benthic community, but some recovery was observed after nine years. Ecological indices used to assess environmental status did not capture the impaired benthic communities caused by the capping. The present study is the first documentation of negative effects of powdered AC on marine benthic communities on a decadal scale. Our results show that the benefits of reduced contaminant bioavailability from capping with AC should be carefully weighed against the cost of long-term detrimental effects on the benthic community. More research is needed to develop a thin-layer capping material that is efficient at sequestering contaminants without being harmful to benthic species.

Assessment of ecological health of Swarnamukhi river estuary, southeast coast of India, through AMBI indices and multivariate tools

A combination of biotic indices, geo-accumulation (I_geo) index, and a multivariate approach were applied to assess the anthropogenic influence on the benthic community at five stations from 2018 to 2019 in the Swarnamukhi river estuary, Nellore, India. Non-metric multidimensional scaling and cluster analysis indicated that the Buckingham canal (BC) station showed azoic conditions and formed a separate cluster. Strong positive factor loadings of Cd (0.96), Al (0.93), Zn (0.91), Fe (0.90), Co (0.89), Cu (0.89), Ni (0.87), Pb (0.85), Cr (0.77), organic matter (0.94), Silt (0.92), and clay (0.93) and negative loading of sand (-0.90) showed the variability in sediment. AMBI results illustrated the disturbance status of each station and classified BC station as 'extremely disturbed' class, and M-AMBI assessed the ecological status as 'bad'. The I_geo index also revealed metal (Cd) contamination. The present study illustrated that the combined approach is effective for ecological assessment of coastal ecosystem.

European aquatic ecological assessment methods: A critical review of their sensitivity to key pressures

The European Union has embarked on a policy which aims to achieve good ecological status in all surface waters (i.e. rivers, lakes, transitional and coastal waters). In theory, ecological status assessment methods should address the effects of all relevant human pressures. In this study, we analyze the degree to which methods European countries use to assess ecological status tackle various pressures affecting European waters. Nutrient pollution is by far the best-covered pressure for all four water categories. Out of total of 423 assessment methods, 370 assess eutrophication and pressure-specific relationships have been demonstrated for 212 of these. "General degradation" is addressed by 238 methods, mostly validated by relationships to combined pressure indices. Other major pressures have received significantly less effort: hydromorphological degradation is assessed by 160 methods and pressure-specific relationships have been demonstrated for just 40 of these. Hydromorphological pressures are addressed (at least by one BQE) only by 25% countries for coastal waters and 70-80% for lakes and transitional waters. Specific diagnostic tools (i.e. single-pressure relationships) for hydromorphology have only been developed by a few countries: only 20% countries have such methods for lakes, coastal and transitional waters and less than half for rivers. Toxic contamination is addressed by 90 methods; however, pressure-specific relationships have been demonstrated for just eight of these. Only two countries have demonstrated pressure-specific acidification methods for rivers, and three for lakes. In summary, methods currently in use mostly address eutrophication and/or general degradation, but there is not much evidence that they reliably pick up the effects of other significant pressures such as hydromorphology or toxic contamination. Therefore, we recommend that countries re-examine: (1) those pressures which affect different water categories in the country; (2) relevant assessment methods to tackle those pressures; (3) whether pressure-response relationships have been developed for each of these.

Multiannual Trend of Micro-Pollutants in Sediments and Benthic Community Response in a Mediterranean Lagoon (Sacca di Goro, Italy)

Long-term variations of ecological status in a Mediterranean coastal lagoon (Sacca di Goro, Northern Adriatic) were investigated, combining data on the concentration of surface sediment contaminants and on the structure of the macrobenthic community. The aim was to assess any amount of chemical contamination and check the response of the macrobenthic community to sediment contamination. Over the studied period, the sediments of the lagoon showed contamination by trace metals and organochlorine pesticides, with most of them exceeding the thresholds indicated by the Italian legislation in many samples. Contamination by polychlorinated dibenzodioxins and dibenzofurans (PCDD/Fs) and polycyclic aromatic hydrocarbons (PAHs) instead never exceeded the threshold. The ecological status based on the macrobenthic community, evaluated through biotic indices (AMBI and M-AMBI), fell below the Good/Moderate threshold in most samples. The results indicate a possible influence of toxic compounds in sediment on benthic organisms, but most of the variability shown by the macrobenthic community is probably due to other factors. The difficulty in establishing a cause/effect relationship was due to the co-occurrence and variability of various stressors (both natural and anthropogenic) and their interactions. The methods currently used for monitoring transitional waters thus seem insufficient to disentangle the effect of pollutants and other environmental variables on the benthos. Integrated approaches (e.g., bioaccumulation and toxicity tests) are thus needed for a more precise identification of the risk posed by a high concentration of pollutants in such environments.

Ecological status assessment based on benthic macrofauna of three Mediterranean ports: Comparisons across seasons, activities and regions

The present study aimed to compare anthropogenic impacts in three Mediterranean ports (Cagliari-Italy, Heraklion-Greece, El-Kantatoui-Tunisia) employing benthic macrofaunal indices, used in the context of the European Water Framework Directive. Sampling stations were selected within ports according to sector usage categorization and sampled over three seasons. Benthic indices calculated include M-AMBI, BENTIX, BQI and BQI_Family. Comparisons were made between the indices values and ecological status (ES) of each station within and between ports. Overall, few statistically significant differences were observed across different seasons or different stations with the same usage within or across ports. The ES of sampling stations in the leisure/fishing and passenger/cargo ships sectors was mostly "good" or "moderate", while the shipyard sector had "poor" ES. The results suggest that the indices used were suitable for assessing the ES of Mediterranean ports, led to comparable results even across different countries and contribute to the adaptation of specific port monitoring guidelines.

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

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

The difficulty of disentangling natural from anthropogenic forcing factors makes the evaluation of ecological quality problematic: A case study from Adriatic lagoons

The complex and dynamic nature of transitional ecosystems pose problems for the assessment of the Ecological Quality Status required by the European Water Framework Directive (WFD; 2000/60/EC). In six Adriatic lagoons, Ecological Quality Status was studied by comparing a biotic index based on macrophytes (MaQI), and three indices based on invertebrates (M-AMBI, M-bAMBI, and ISD). Ecological Status evaluated though MaQI and ISD resulted in quite degraded ecosystems (moderate/poor/bad), with only opportunistic algae and macrobenthic communities dominated by small size classes. Those results were supported by physico-chemical parameters, indicating high nutrients inputs, and anthropogenic pressures related with agriculture and fishery activities. Ecological Status obtained with M-AMBI and M-bAMBI was higher, with some sites reaching even the "good" status. The best response to anthropogenic pressures, in terms of a pressure index, was obtained by M-AMBI and M-bAMBI. Nevertheless, the response of used metrics (such as AMBI and bAMBI) to environmental variables not related to anthropogenic impact, and the high heterogeneity of physical-chemical conditions within lagoons, represent potential problems for the correct evaluation of Ecological Status of transitional waters. When different metrics give different responses it becomes a problem for managers who cannot easily make a decision on the remedial measures. The disagreement among indices arose because of the different response of biological elements to different stressors, and because the different indices based on macroinvertebrates focused on different aspects of the community, providing complementary information. So urge the need to find alternative approaches for a correct assessment of Ecological Status, with the combination of different biological elements, and considering the development of new indices (e.g. M-bAMBI) or refinement of the existing ones.

Forever young: The successful story of a marine biotic index

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.

Beyond classic ecological assessment: The use of functional indices to indicate fish assemblages sensitivity to human disturbance in estuaries

Assessing ecological health of aquatic ecosystems is crucial in the current context of biodiversity loss to guide and prioritize management actions. Although several fish-based indices were developed to assess the ecological status of estuarine ecosystems, they do not provide guidance on the causal responses of communities to disturbances. The functional trait-based approach provides an understanding of how human disturbance affects the composition of biological and ecological traits in assemblages, as well as their consequences for ecosystem functioning. Here, we evaluate the responses of fish assemblages to human disturbance in 30 French estuaries using several taxonomic and functional indices (e.g. diversity, evenness or redundancy). We tested whether these indices can provide additional information on the human impacts and health of assemblages that are not reflected by the ecological indicator (fish-based index ELFI). Results indicated that high values of local human disturbances were associated to a decrease in fish abundance, decrease in species richness and reduced functional redundancy, whereas taxonomic and functional evenness increased. In contrast, the functional richness remained stable suggesting that the functional traits of species removed by stressors were maintained by more tolerant species. Indeed, we found that the local disturbances mainly resulted in a decrease in the proportions of small benthic species feeding on macro-invertebrates, which were dominant in the studied estuaries. Some functional alterations were detected by the fish-based index, but the decline of functional redundancy was not reflected, highlighting a serious concern for management. Indeed, the abrupt collapse of functional redundancy in response to local disturbances can decrease the ability of assemblages to maintain certain species traits in the face of future environmental disturbance, including climate change. From a management perspective, the application of such functional redundancy measure in monitoring programs can help stakeholders identify sensitive areas where conservation efforts need to be planned.

Heavy metals, OCPs, PAHs, and PCDD/Fs contamination in surface sediments of a coastal lagoon (Valli di Comacchio, NW Adriatic, Italy): Long term trend (2002-2013) and effect on benthic community

Surface sediments contamination (heavy metals, organochlorine pesticides, polycyclic aromatic hydrocarbons, polychlorinated dibenzodioxins and dibenzofurans) and benthic community of the Valli di Comacchio, were analysed from 2002 to 2013. Along the studied period, most of analysed pollutants did not exceed thresholds for Good chemical status of sediments. In 2008, a peak of contamination was observed, with total PAHs and OCPs exceeding their threshold. Considering metals, Ni and Cr exceeded their thresholds, but not the background levels for the area, suggesting natural enrichment; conversely Pb exceeded background levels for the area in many samples, but it exceeded its sediment quality thresholds only in few samples (2006, 2009, 2011). Conversely, the ecological status evaluated though AMBI and M-AMBI, was below the Good/Moderated thresholds established by WFD in most of the studied years. In the 11 yrs-study period, the benthic community showed a very weak response to chemical contamination.

Comparison of benthic indices for the evaluation of ecological status of three Slovenian transitional water bodies (northern Adriatic)

Benthic indicators are important tools for the classification of coastal and transitional water bodies. The aim of the work was to assess for the first time the Environmental Status (ES) of Slovenian transitional waters, comparing the following biotic indices: richness, Shannon-Weaver diversity, AMBI, M-AMBI, BENTIX and BITS indices. A total of 13 stations were sampled with a Van Veen grab, in three ecosystems in the northern Adriatic. Samples were sieved and sorted, invertebrates identified and counted. The anthropogenic impact was estimated with professional judgement. Richness and diversity showed a good response to anthropogenic pressure. Conversely, indices based on sensitivity/tolerance groups did not showed a clear distinction between more and less impacted ecosystems. In particular BENTIX underestimated the ES, while with BITS there was a overestimation. The best evaluation was obtained with M-AMBI, because even if based on a sensitivity/tolerance approach, it considered also the structural aspect of the community.

Assessing the ecological status of Italian lagoons using a biomass-based index

We compared the performance of abundance- and biomass-based M-AMBI in the 13 major Italian lagoons, using a benthic dataset constituted by 208 sampling sites. The relative importance of ecological groups changed when using abundance or biomass, sometimes leading to an improved ecological status classification. Being biomass more ecologically relevant than abundance, the adoption of a biomass-based index may better describe the ecological status of lagoons, where the community is naturally disturbed and dominated by tolerant and opportunist species.

Impact of kelp cultivation on the Ecological Status of benthic habitats and Zostera marina seagrass biomass

The Ecological Status of subtidal benthic communities within a commercial kelp farm on the southwest coast of Ireland was not impacted by macroalgal cultivation. Additionally, there was no effect on the biomass of Zostera marina, a key habitat under the EU Habitats Directive and OSPAR Commission. However, sediment grain size and total organic matter (TOM) were influenced by abiotic and biotic aspects of the farm. A temporal effect on univariate and multivariate species data, Infaunal Quality Index (IQI) and Z. marina biomass was observed. This effect was likely a community response to high storm disturbance in winter 2013/14. The use of IQI to assess the impact of macroalgal cultivation on benthic communities is a novel approach. This study supports a view that environmental impacts of macroalgal cultivation are relatively benign compared to other forms of aquaculture. Further research must be conducted to understand all interactions between aquaculture activities and the environment.

The status and characteristics of eutrophication in tropical coastal water

A set of methodological tools was tested to assess the sensitivity of several ecological and biological indices to eutrophication while at the same time attempting to explore a linkage among pressures, classification assessment and drivers. Industrial discharges, harbor activities, natural interactions and river discharges are the pressures most related to the eutrophication process in tropical coastal water bodies. Among the eutrophication indices used, TRIX and operational indicators overestimated the eutrophication status in the study area, but EI and chl-a seems to be a rather responsive index to reflect the first stage of eutrophication. It is noteworthy that EI and chl-a showed better overall agreement with the ecological quality status (EcoQ) showing that probably it reflects the indirect relation of macrobenthic with water eutrophication in a better way. An ecological boundary of EI and chl-a from moderate to poor may be needed in order to explain the poor status of relatively eutrophic Klang Strait coastal sites.

The well sorted fine sand community from the western Mediterranean Sea: A resistant and resilient marine habitat under diverse human pressures

The Biocoenosis of Well Sorted Fine Sands (WSFS) (SFBC, Sables Fins Bien Calibrés in French) is a Mediterranean community very well delimited by bathymetry (2-25 m) and sedimentology (>90% of fine sand) occurring in zones with relatively strong hydrodynamics. In this study focused on sites located along the Algerian, French, Italian and Spanish coasts of the Western Basin of the Mediterranean Sea (WBMS) we aim to compare the structure, ecological status and diversity of the macrofauna of the WSFS and examine the effects of recent human pressures on the state of this shallow macrobenthic community. We assess the ecological status and functioning of these WSFS using three categories of benthic indices: a) five indices based on classification of species into ecological groups, AMBI, BO2A, BPOFA, IQ and IP, b) the ITI index based on classification of species in trophic groups, and c) the Shannon H' index, and the Biological Traits Analysis (BTA), which is an alternative method to relative taxon composition analysis and integrative indices. Cluster analyses show that each zone show a particular taxonomic richness and dominant species. The seven benthic indices reveal that the macrobenthos of the WSFS of the four coastal zones show good or high Quality Status, except for one location on the Algerian coast (the Djendjen site) in 1997. BTA highlights the presence of three groups of species: 1) typical characteristic species; 2) indicator species of enrichment of fine particles and organic matter, and 3) coarse sand species which are accessorily found on fine sand. Finally, the WSFS which are naturally subject to regular natural physical perturbations show a high resilience after human pressures but are very sensitive to changes in the input of organic matter.

Impact of prolonged storm activity on the Ecological Status of intertidal benthic habitats within oyster (Crassostrea gigas) trestle cultivation sites

The Ecological Status (ES; sensu the Water Framework Directive) of intertidal benthic communities within six oyster trestle cultivation sites was found to be negatively impacted along the access routes to trestles in a 2013 study. All cultivation sites occur within Natura 2000 sites. The current study revisited four of the 2013 cultivation sites in February 2014 one month after the storm activity of winter 2013/14 to test if the compaction effect along access routes persisted after the storms. Three levels of the fixed factor treatment were sampled; immediately below the trestles, along the access route and 300m away from any anthropogenic activity. The compaction effect at the Access treatment persisted in spite of the major storm activity. The current study showed the IQI to be effective for assessing the impacts of aquaculture and highlights the IQI as a tool for monitoring Conservation Status of intertidal communities under the Habitats Directive.

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.

Testing the efficiency of temperate benthic biotic indices in assessing the ecological status of a tropical ecosystem

The objectives of the present study were to evaluate the ecological status of tropical coastal waters using the temperate benthic indices and examine the effect of seasonal variability on the performance of benthic indices. Macrobenthic samples were collected from northwest to southeast coast of India during 2003-2012 and we tested different univariate indices, ecological strategies, indicator species and multimetric indices. AMBI and multimetric indices performed satisfactorily in evaluating the ecological status. Seasonal variability on the biotic indices was observed during the southwest monsoon and fall intermonsoon period due to recruitment. Therefore, we recommended the non-monsoon period (January-May) as a suitable time of the year to use the indices for effective assessment of the Indian coastal waters. Results show that, the temperate benthic indices are efficient in assessing the tropical environmental status. However, complementary use of different indices is suggested for accurate assessment of the environmental status.

Long-term (1998-2010) large-scale comparison of the ecological quality status of gulf of lions (NW Mediterranean) benthic habitats

A comprehensive Mediterranean data set has been used to address 3 questions associated with the use of sensitivity/tolerance based biotic indices to infer the Ecological Quality status (EcoQs) of benthic habitats. Our results showed: (1) a significant effect of the reference database on derived sensitivity/tolerance measure (ES500.05) as well as associated Benthic Quality Index values and derived EcoQs; (2) a lack of correlation neither between BQI and AZTI Marine Biotic Index values nor between BQI and Multivariate-AZTI Marine Biotic Index values; (3) a lack of correlation between the values of the Benthic Habitat Quality Index (index derived from Sediment Profile Imagery) and those of either of the 3 tested biotic indices; and (4) a general agreement between the 3 tested biotic indices in describing the lack of global trend for the EcoQs of the Gulf of Lions despite the occurrence of significant changes in benthic macrofauna composition between 1998 and 2010.

Quantified biotic and abiotic responses to multiple stress in freshwater, marine and ground waters

We reviewed 219 papers and built an inventory of 532 items of ecological evidence on multiple stressor impacts in rivers, lakes, transitional and coastal waters, as well as groundwaters. Our review revealed that, despite the existence of a huge conceptual knowledge base in aquatic ecology, few studies actually provide quantitative evidence on multi-stress effects. Nutrient stress was involved in 71% to 98% of multi-stress situations in the three types of surface water environments, and in 42% of those in groundwaters. However, their impact manifested differently along the groundwater-river-lake-transitional-coastal continuum, mainly determined by the different hydro-morphological features of these ecosystems. The reviewed papers addressed two-stressor combinations most frequently (42%), corresponding with the actual status-quo of pressures acting on European surface waters as reported by the Member States in the WISE WFD Database (EEA, 2015). Across all biological groups analysed, higher explanatory power of the stress-effect models was discernible for lakes under multi-stressor compared to single stressor conditions, but generally lower for coastal and transitional waters. Across all aquatic environments, the explanatory power of stress-effect models for fish increased when multi-stressor conditions were taken into account in the analysis, qualifying this organism group as a useful indicator of multi-stress effects. In contrast, the explanatory power of models using benthic flora decreased under conditions of multiple stress.

Mussel farming in Maliakos Gulf and quality indicators of the marine environment: Good benthic below poor pelagic ecological status

Biological and geochemical variables in the water column and sediments were monitored along a transect of a mussel farm located in a transitional environment in Maliakos Gulf, a semi-enclosed gulf in eastern Mediterranean. Analyses of water, sediment and macrofauna samples were used to calculate ecological status indicators in the context of the European Water Framework Directive. The water column ecological status was "Poor" or "Bad" showing little change with distance from the farm, but the ecological status of the benthic communities was found to be "Good," although there were quantitative changes in macrofaunal indices with distance from the farm.

Efficacy of single and multi-metric fish-based indices in tracking anthropogenic pressures in estuaries: An 8-year case study

Facing a generalized increase in water degradation, several programmes have been implemented for protecting and enhancing the water quality and associated wildlife, which rely on ecological indicators to assess the degree of deviation from a pristine state. Here, single (species number, Shannon-Wiener H', Pielou J') and multi-metric (Estuarine Fish Assessment Index, EFAI) community-based ecological quality measures were evaluated in a temperate estuary over an 8-year period (2005-2012), and established their relationships with an anthropogenic pressure index (API). Single metric indices were highly variable and neither concordant amongst themselves nor with the EFAI. The EFAI was the only index significantly correlated with the API, indicating that higher ecological quality was associated with lower anthropogenic pressure. Pressure scenarios were related with specific fish community composition, as a result of distinct food web complexity and nursery functioning of the estuary. Results were discussed in the scope of the implementation of water protection programmes.

One Step forward: Benthic Pelagic Coupling and Indicators for Environmental Status

A large data set from the Eastern Mediterranean was analyzed to explore the relationship between seawater column variables and benthic community status. Our results showed a strong quantitative link between the seawater column variables (Chlorophyll a and Eutrophication Index) and various indicators describing benthic diversity and community composition. The percentage of benthic opportunistic species increased significantly in the stations with high trophic status of the seawater column and so did the strength of the coupling between values of seawater column and benthic indicators. The Eutrophication Index threshold level of 0.85, separating the “Bad and Poor” from “Moderate to High” conditions could serve as an acceptable critical value above which there is a readily observable change in benthic community composition.

Is there a possibility of ranking benthic quality assessment indices to select the most responsive to different human pressures?

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.

Spatial variability of three benthic indices for marine quality assessment in a subtropical estuary of Southern Brazil

Indices based on macrobenthic responses to disturbance remain to be adequately tested for the detection of spatial variability by robust sampling designs. We present herein a congruence test to real-world data of the widely used indices AMBI, M-AMBI and BENTIX in tidal flats of a subtropical estuary. We used a hierarchical sampling design to evaluate the spatial variability of the indices in response to distinct levels of sewage contamination. Indices were then tested for correlations with chemical proxies of contamination and for the similarity of responses. BENTIX and M-AMBI produced over- and underestimations of ecological status. We found a low degree of similarity among indices as an expression of the spatial variation of macrofaunal assemblages on their performances. Only AMBI varied at the contamination scale (10(3)m) and was congruent with physical-chemical proxies. Ambiguous responses indicated effects of natural inputs of organic matter rather than environmental quality associated to sewage.

Response of multi-metric indices to anthropogenic pressures in distinct marine habitats: the need for recalibration to allow wider applicability

Sustainable exploitation of coastal ecosystems is facilitated by tools which allow reliable assessment of their response to anthropogenic pressures. The Infaunal Quality Index (IQI) and Multivariate-AMBI (M-AMBI) were developed to classify the ecological status (ES) of benthos for the Water Framework Directive (WFD). The indices respond reliably to the impacts of organic enrichment in muddy sand habitats, but their applicability across a range of pressures and habitats is less well understood. The ability of the indices to predict changes in response to pressures in three distinct habitats, intertidal muddy sand, maerl and inshore gravel, was tested using pre-existing datasets. Both responded following the same patterns of variation as previously reported. The IQI was more conservative when responding to environmental conditions so may have greater predictive value in dynamic habitats to provide an early-warning system to managers'. Re-calibration of reference conditions is necessary to reliably reflect ES in different habitats.

A mixed modeling approach to predict the effect of environmental modification on species distributions

Human infrastructures can modify ecosystems, thereby affecting the occurrence and spatial distribution of organisms, as well as ecosystem functionality. Sustainable development requires the ability to predict responses of species to anthropogenic pressures. We investigated the large scale, long term effect of important human alterations of benthic habitats with an integrated approach combining engineering and ecological modelling. We focused our analysis on the Oosterschelde basin (The Netherlands), which was partially embanked by a storm surge barrier (Oosterscheldekering, 1986). We made use of 1) a prognostic (numerical) environmental (hydrodynamic) model and 2) a novel application of quantile regression to Species Distribution Modeling (SDM) to simulate both the realized and potential (habitat suitability) abundance of four macrozoobenthic species: Scoloplos armiger, Peringia ulvae, Cerastoderma edule and Lanice conchilega. The analysis shows that part of the fluctuations in macrozoobenthic biomass stocks during the last decades is related to the effect of the coastal defense infrastructures on the basin morphology and hydrodynamics. The methodological framework we propose is particularly suitable for the analysis of large abundance datasets combined with high-resolution environmental data. Our analysis provides useful information on future changes in ecosystem functionality induced by human activities.

Polychaete richness and abundance enhanced in anthropogenically modified estuaries despite high concentrations of toxic contaminants

Ecological communities are increasingly exposed to multiple chemical and physical stressors, but distinguishing anthropogenic impacts from other environmental drivers remains challenging. Rarely are multiple stressors investigated in replicated studies over large spatial scales (>1000 kms) or supported with manipulations that are necessary to interpret ecological patterns. We measured the composition of sediment infaunal communities in relation to anthropogenic and natural stressors at multiple sites within seven estuaries. We observed increases in the richness and abundance of polychaete worms in heavily modified estuaries with severe metal contamination, but no changes in the diversity or abundance of other taxa. Estuaries in which toxic contaminants were elevated also showed evidence of organic enrichment. We hypothesised that the observed response of polychaetes was not a ‘positive’ response to toxic contamination or a reduction in biotic competition, but due to high levels of nutrients in heavily modified estuaries driving productivity in the water column and enriching the sediment over large spatial scales. We deployed defaunated field-collected sediments from the surveyed estuaries in a small scale experiment, but observed no effects of sediment characteristics (toxic or enriching). Furthermore, invertebrate recruitment instead reflected the low diversity and abundance observed during field surveys of this relatively ‘pristine’ estuary. This suggests that differences observed in the survey are not a direct consequence of sediment characteristics (even severe metal contamination) but are related to parameters that covary with estuary modification such as enhanced productivity from nutrient inputs and the diversity of the local species pool. This has implications for the interpretation of diversity measures in large-scale monitoring studies in which the observed patterns may be strongly influenced by many factors that covary with anthropogenic modification.

Ecological status assessment and response of benthic communities to environmental variability: the Valli di Comacchio (Italy) as a study case

The Valli di Comacchio is one of most representative choked (not influenced by the tidal regime) lagoons in the Mediterranean and Europe. We compared the ecological status (ES) classification (sensu European Water Framework Directive, 2000/60/EC) of the Valli obtained through supporting physicochemical elements and biotic indices. The variability of water parameters was investigated through 1997-2002 at 4 permanent sampling stations. During the six years of investigation, macrobenthic data were collected to identify the response of several biological indices (taxonomic, functional and ecological). ES classification through supporting physicochemical elements resulted in discordant patterns. Nor taxonomic neither functional measures were able to add more information than that given by univariate biodiversity measures. Gaps and bias of the indices used were identified. Due to the absence of well defined environmental gradients, taxonomic and functional measures loose most of their usefulnesses. ES classification through ecological indices (M-AMBI and BITS) resulted in quite a concordant pattern, although BITS underestimated ES when there was a strong dominance of one opportunist family in the benthic community.

Comparison of granulometric methods and sampling strategies used in marine habitat classification and Ecological Status assessment

Sediment particle size analysis (PSA) is routinely used to support benthic macrofaunal community distribution data in habitat mapping and Ecological Status (ES) assessment. No optimal PSA Method to explain variability in multivariate macrofaunal distribution has been identified nor have the effects of changing sampling strategy been examined. Here, we use benthic macrofaunal and PSA grabs from two embayments in the south of Ireland. Four frequently used PSA Methods and two common sampling strategies are applied. A combination of laser particle sizing and wet/dry sieving without peroxide pre-treatment to remove organics was identified as the optimal Method for explaining macrofaunal distributions. ES classifications and EUNIS sediment classification were robust to changes in PSA Method. Fauna and PSA samples returned from the same grab sample significantly decreased macrofaunal variance explained by PSA and caused ES to be classified as lower. Employing the optimal PSA Method and sampling strategy will improve benthic monitoring.

Critical appraisal on the identification of Reference Conditions for the evaluation of ecological quality status along the Emilia-Romagna coast (Italy) using M-AMBI

According to the European Water Framework Directive, the ecological status (ES) of a water body is determined by comparing observation data with undisturbed Reference Conditions (RCs). Defining RCs is crucial when evaluating the ES of a water body as it strongly affects the final outcome of any index application. Identifying RCs by observing real sites is not feasible in many marine environments, such as the Emilia-Romagna coast (Italy, N-Adriatic Sea). We used a statistical approach on a large dataset to derive RCs for the application of the benthic index M-AMBI in this area. We then applied M-AMBI to samples collected along a gradient of presumed environmental disturbance. The results put 14.8% of the Emilia-Romagna samples in "High" ES, 60.2% in "Good", 23.0% in "Moderate" and 2.0% in "Poor", showing a spatial gradient of improving quality. These results are in agreement with the extensive ecological knowledge available for this area.

Coastal defence through low crested breakwater structures: jumping out of the frying pan into the fire?

The Adriatic coast of Punta Marina (Ravenna) is protected by 3-km long low crested breakwater structures (LCSs). Through a 3-years long multidisciplinar study, we assessed the impact of such defensive structures on environmental and biological condition. LCSs create pools where conditions are very different from the surrounding nearshore system. Mechanical disturbance by currents and waves varied greatly in intensity and frequency between seaward and landward sides of the structures. Sedimentary budget was positive at the landward side, but it was due to a gain on the seafloor and not on the emerged beach. The budget at seaward was negative. LCSs determine differences in benthic assemblages, alter the seasonal pattern of communities, and modify seasonal fluctuations of animal assemblages. Landward sheltered areas can be seen as "lagoonal island" surrounded by a "sea of marine habitat". Differences in ecological quality status, obtained through M-AMBI, are due to the sum of these factors.