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

An ecological status indicator for all time: Are AMBI and M-AMBI effective indicators of change in deep time?

Increasingly environmental management seeks to limit the impacts of human activities on ecosystems relative to some 'reference' condition, which is often the presumed pre-impacted state, however such information is limited. We explore how marine ecosystems in deep time (Late Jurassic) are characterised by AZTI's Marine Biotic Index (AMBI), and how the indices responded to natural perturbations. AMBI is widely used to detect the impacts of human disturbance and to establish management targets, and this study is the first application of these indices to a fossil fauna. Our results show AMBI detected changes in past seafloor communities (well-preserved fossil deposits) that underwent regional deoxygenation in a manner analogous to those experiencing two decades of organic pollution. These findings highlight the potential for palaeoecological data to contribute to reconstructions of pre-human marine ecosystems, and hence provide information to policy makers and regulators with greater temporal context on the nature of 'pristine' marine ecosystems.

Putting on a bow-tie to sort out who does what and why in the complex arena of marine policy and management

Marine policy and management has to cope with a plethora of human activities that cause pressures leading to changes to the natural and human systems. Accordingly, it requires many policy and management responses to address traditional, cultural, social, ecological, technical, and economic policy objectives. Because of this, we advocate that a fully-structured approach using the IEC/ISO 31010 Bow-tie analysis will allow all elements to be integrated for a cost-effective system. This industry-standard system, described here with examples for the marine environment, will fulfil many of the demands by the users and uses of the marine system and the regulators of those users and uses. It allows for bridging several aspects: the management and environmental sciences, the management complexity and governance demands, the natural and social sciences and socio-economics and outcomes. Most importantly, the use of the Bow-tie approach bridges systems analysis and ecosystem complexity. At a time when scientific decisions in policy making and implementation are under question, we conclude that it provides a rigorous, transparent and defendable system of decision-making.

Translating Ecological Integrity terms into operational language to inform societies

It is crucial that societies are informed on the risks of impoverished ecosystem health for their well-being. For this purpose, Ecological Integrity (EI) is a useful concept that seeks to capture the complex nature of ecosystems and their interaction with social welfare. But the challenge remains to measure EI and translate scientific terminology into operational language to inform society. We propose an approach that simplifies marine ecosystem complexity by applying scientific knowledge to identify which components reflect the state or state change of ecosystems. It follows a bottom-up structure that identifies, based on expert knowledge, biological components related with past and present changing conditions. It is structured in 5 stages that interact in an adaptive way: stage 1, in situ observations suggest changes could be happening; stage 2 explores available data that represent EI; stage 3, experts' workshops target the identification of the minimum set of variables needed to define EI, or the risk of losing EI; an optative stage 4, where deviance from EI, or risk of deviance, is statistically assessed; stage 5, findings are communicated to society. We demonstrate the framework effectiveness in three case studies, including a data poor situation, an area where lack of reference sites hampers the identification of historical changes, and an area where diffuse sources of stress make it difficult to identify simple relationships with of ecological responses. The future challenge is to operationalise the approach and trigger desirable society actions to strengthen a social-nature link.

Disentangling settlement responses to nutrient-rich contaminants: Elevated nutrients impact marine invertebrate recruitment via water-borne and substrate-bound cues

Anthropogenic contaminants, including nutrient enrichment, frequently alter environmental conditions in marine systems and affect the development of communities on hard-substrata. Biofilms can influence the settlement of marine invertebrates and hence impact on the structure of fouling communities. Few studies have examined bacteria, invertebrates and nutrient-rich contaminants in concert, with none yet to examine the effects of nutrient-rich contaminants on both biofilms and the recruitment of sessile invertebrate communities in-situ to ascertain the mechanistic basis behind observed impacts. Biofilm treatments were allowed to develop under manipulated environmental conditions of either ambient or enriched nutrient levels. Enrichment conditions were elevated via slow-release fertiliser and invertebrate recruitment was prevented during initial biofilm development. Biofilm treatments (including a no film control) were then subject to either ambient or enriched water-borne nutrients (in a fully-factorial design) during a period of invertebrate colonisation in the field. Effects of nutrient-rich contaminants on invertebrate recruitment were observed as changes to community composition and the abundances of taxonomic groups. Communities on no biofilm control treatments differed from those with pre-developed biofilms. Naturally developed biofilms promoted recruitment by all organisms, except barnacles, which preferred nutrient-enriched biofilms. Water-borne nutrients increased the recruitment of ascidians and barnacles, but suppressed bryozoan, serpulid polychaete and sponge recruitment. The direct and indirect impacts observed on biofilm and invertebrate communities suggest that increasing nutrient levels via nutrient-rich contaminants will result in structural community shifts that may ultimately impact ecosystem functioning within estuaries.

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.

Chesapeake Bay's water quality condition has been recovering: Insights from a multimetric indicator assessment of thirty years of tidal monitoring data

To protect the aquatic living resources of Chesapeake Bay, the Chesapeake Bay Program partnership has developed guidance for state water quality standards, which include ambient water quality criteria to protect designated uses (DUs), and associated assessment procedures for dissolved oxygen (DO), water clarity/underwater bay grasses, and chlorophyll-a. For measuring progress toward meeting the respective states' water quality standards, a multimetric attainment indicator approach was developed to estimate combined standards attainment. We applied this approach to three decades of monitoring data of DO, water clarity/underwater bay grasses, and chlorophyll-a data on annually updated moving 3-year periods to track the progress in all 92 management segments of tidal waters in Chesapeake Bay. In 2014-2016, 40% of tidal water segment-DU-criterion combinations in the Bay (n = 291) are estimated to meet thresholds for attainment of their water quality criteria. This index score marks the best 3-year status in the entire record. Since 1985-1987, the indicator has followed a nonlinear trajectory, consistent with impacts from extreme weather events and subsequent recoveries. Over the period of record (1985-2016), the indicator exhibited a positive and statistically significant trend (p < 0.05), indicating that the Bay has been recovering since 1985. Patterns of attainment of individual DUs are variable, but improvements in open water DO, deep channel DO, and water clarity/submerged aquatic vegetation have combined to drive the improvement in the Baywide indicator in 2014-2016 relative to its long-term median. Finally, the improvement in estimated Baywide attainment was statistically linked to the decline of total nitrogen, indicating responsiveness of attainment status to the reduction of nutrient load through various management actions since at least the 1980s.

Land use change modeling through scenario-based cellular automata Markov: improving spatial forecasting

Efficient land use management requires awareness of past changes, present actions, and plans for future developments. Part of these requirements is achieved using scenarios that describe a future situation and the course of changes. This research aims to link scenario results with spatially explicit and quantitative forecasting of land use development. To develop land use scenarios, SMIC PROB-EXPERT and MORPHOL methods were used. It revealed eight scenarios as the most probable. To apply the scenarios, we considered population growth rate and used a cellular automata-Markov chain (CA-MC) model to implement the quantified changes described by each scenario. For each scenario, a set of landscape metrics was used to assess the ecological integrity of land use classes in terms of fragmentation and structural connectivity. The approach enabled us to develop spatial scenarios of land use change and detect their differences for choosing the most integrated landscape pattern in terms of landscape metrics. Finally, the comparison between paired forecasted scenarios based on landscape metrics indicates that scenarios 1-1, 2-2, 3-2, and 4-1 have a more suitable integrity. The proposed methodology for developing spatial scenarios helps executive managers to create scenarios with many repetitions and customize spatial patterns in real world applications and policies.

Sensitivity of indicators matters when using aggregation methods to assess marine environmental status

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.

Improving the implementation of marine monitoring in the northeast Atlantic

Marine monitoring in the northeast Atlantic is delivered within identifiable monitoring themes, established through time and defined by the geographical area and policy drivers they serve, the sampling methodologies they use, their assessment methodologies, their funding and governance structures and the people or organisations involved in their implementation. Within a monitoring theme, essential components for effective monitoring are governance, strategy and work plan, sampling protocols, quality assurance, and data and assessment structures. This simple framework is used to analyse two monitoring theme case studies; national ecosystem health monitoring, and regional fish stock monitoring. Such essential component analyses, within marine monitoring themes, can help improve monitoring implementation by identifying gaps and overlaps. Once monitoring themes are recognised, explicitly defined and streamlined, travel towards integrated monitoring may be made easier as the current lack of clarity in thematic marine monitoring implementation is one barrier to integration at both national and regional scales.

Chesapeake Bay Dissolved Oxygen Criterion Attainment Deficit: Three Decades of Temporal and Spatial Patterns

Low dissolved oxygen (DO) conditions are a recurring issue in waters of Chesapeake Bay, with detrimental effects on aquatic living resources. The Chesapeake Bay Program partnership has developed criteria guidance supporting the definition of state water quality standards and associated assessment procedures for DO and other parameters, which provides a binary classification of attainment or impairment. Evaluating time series of these two outcomes alone, however, provides limited information on water quality change over time or space. Here we introduce an extension of the existing Chesapeake Bay water quality criterion assessment framework to quantify the amount of impairment shown by space-time exceedance of DO criterion ("attainment deficit") for a specific tidal management unit (i.e., segment). We demonstrate the usefulness of this extended framework by applying it to Bay segments for each 3-year assessment period between 1985 and 2016. In general, the attainment deficit for the most recent period assessed (i.e., 2014-2016) is considerably worse for deep channel (DC; n = 10) segments than open water (OW; n = 92) and deep water (DW; n = 18) segments. Most subgroups - classified by designated uses, salinity zones, or tidal systems - show better (or similar) attainment status in 2014-2016 than their initial status (1985-1987). Some significant temporal trends (p < 0.1) were detected, presenting evidence on the recovery for portions of Chesapeake Bay with respect to DO criterion attainment. Significant, improving trends were observed in seven OW segments, four DW segments, and one DC segment over the 30 3-year assessment periods (1985-2016). Likewise, significant, improving trends were observed in 15 OW, five DW, and four DC segments over the recent 15 assessment periods (2000-2016). Subgroups showed mixed trends, with the Patuxent, Nanticoke, and Choptank Rivers experiencing significant, improving short-term (2000-2016) trends while Elizabeth experiencing a significant, degrading short-term trend. The general lack of significantly improving trends across the Bay suggests that further actions will be necessary to achieve full attainment of DO criterion. Insights revealed in this work are critical for understanding the dynamics of the Bay ecosystem and for further assessing the effectiveness of management initiatives aimed toward Bay restoration.

Assessing watercourse quality: challenges in implementing European and Swiss legal frameworks

Hydro-climatic changes and the increasing release of pollutants into rivers by human activities tend to affect the quality of watercourses, to alter aquatic ecosystems and to reduce the amount of useable water. The ecological and chemical states of rivers and their evolution is thus of growing concern. In Europe and Switzerland, water policies are progressively shifting towards a holistic approach of river systems. The European Commission notably established a framework to highlight rivers' ecological deficits and to enhance regional or local water management plans. In Switzerland, a similar framework is currently under development. In this paper, both procedures are compared and implemented in a Swiss catchment dominated by agricultural activities. The aim is to define the challenges that still need to be addressed to assess and sustain river health. The hydromorphological, ecological, and ecotoxicological quality of the river was evaluated. Both frameworks highlighted the fact that no section of the river can currently be classified as being in a good environmental state and that the state deteriorates as tributaries and wastewater discharge flow into the main riverbed. Chemical issues and water quality changes due to hydro-climatic variations and management strategies were also pinpointed. Both frameworks are thus useful tools to survey changes in rivers quality in space and over time. However, challenges remain regarding the appropriate strategies to monitor and analyze chemicals, the definition of target values and conditions, the evaluation and integration of human-induced pressures, and the overall evaluation of the state of a river. The development of integrated indicators or of ecosystem services approaches is considered as a potential solution to explore river health and to define efficient restoration measures by water managers.

Benthic pelagic coupling in a mesocosm experiment: Delayed sediment responses and regime shifts

A mesocosm experiment was performed to study benthic-pelagic coupling under a eutrophication gradient. Nine mesocosms were deployed in the facilities of the Hellenic Center for Marine Research in Crete, in the Eastern Mediterranean. The mesocosms were 4m deep, containing 1.5m³ of coastal water and, at the bottom, they included 85l of undisturbed sediment, collected from a semi-impacted area in the port of Heraklion, Crete. A eutrophication gradient was created by adding nutrients in the water column (Low and High) and the experiment lasted 58days. Water column and sediment environmental variables were measured at regular intervals. The results indicate that sedimentation caused by eutrophication in the water column affected sediment geochemical variables but in most cases a time lag was observed between the trophic status of the water column and the response of the sediment. Additionally, in the High eutrophication treatment, several fluctuations were observed and the system did not recover within the experimental duration, as opposed to the Low treatment which showed fewer fluctuations and signs of recovery.

Spatial patterns and temporal trends of trace metal mass budgets in the western Adriatic sediments (Mediterranean Sea)

Spatial patterns of major (Al, Fe and Ti) and trace metals (Cu, Cr, Mn, Ni, Pb and Zn) measured in surficial sediments collected within the Late-Holocene mud-wedge in the western Adriatic Sea were analyzed to elucidate their sources, transport and mass budgets. Distributions of sedimentary trace metals, their fluvial inputs and accumulation loads reveal along-shore transport towards the southern Adriatic. Pb and to a lower extent Zn accumulation loads over time decreased significantly since 1988 in the North Adriatic, consistently with the implementation of regulations in the Western Europe, whereas Zn accumulation in the Po River prodelta remained unchanged since 1995. The Po River fluvial inputs accounted for half of Cr, Ni, Pb and Zn of the fluvial inputs into the western Adriatic Sea, contributing for the delivery of important amounts of Cr and Ni into the sediments, probably related to the natural occurrence of ultramafic rocks in the North sector. Collectively, ~30% of trace metal fluvial inputs discharged into the North sector are exported to the Central and South sectors. The Po River acts as both a bypass and an accumulation zone. In contrast, trace metal accumulation in the Central sector far exceed trace metal fluvial inputs, which suggested that this area is a preferential sink for particle-reactive river-borne material from the North Adriatic. The North sector shows moderate enrichment of Zn and Pb mainly related to the Po River influence. The anthropogenic fraction of Pb shows a large drop of ~30% from the North sector southwards, whereas Zn proportions remain fairly the same up to the Central sector only decreasing in the South sector.

Can the leaf-bag technique detect benthic macrofauna responses to sediment contamination by metals and metalloids in estuaries?

The Estarreja Channel, Ria de Aveiro, Portugal, received industrial effluents for over 70years. Despite the discharges stopped a decade ago, a recent study showed negative ecological effects still associated with the metal and metalloid contaminated sediments. In contaminated versus reference channels, this study compared the benthic macrofauna collected with corer and mesh-bags for community structure and synthesis descriptors, namely taxa richness (S), Shannon-Wiener diversity (H'), taxonomic (AMBI and M-AMBI) and non-taxonomic (ISS) biotic indices and functional indicators (decomposition rates). The corer infauna dominated community and the associated S, H', M-AMBI and ISS indices detected significant differences between contaminated and reference channels, otherwise undistinguished by the decomposition rates and the mesh-bags epifauna dominated community and associated indices. This suggests that sediment contamination in the deeper layers is not being transferred to the surface layers, explaining the non-affectation of the benthic macrofauna communities sampled in the leaf-bags.

Development and validation of a bacteria-based index of biotic integrity for assessing the ecological status of urban rivers: A case study of Qinhuai River basin in Nanjing, China

With the increasing human disturbance to urban rivers, the extinction and biodiversity losses of some macroorganism species decreased the accuracy of bioassessment. In this study, a novel index of biotic integrity based on bacteria (Ba-IBI) was first developed for Qinhuai River in Nanjing city, China. Thirty-two biofilm samples were collected along the river bank and the bacterial communities were identified by high-throughput sequencing. By the range, responsive, and redundancy tests, four core metrics were selected from the dataset of 78 candidate metrics, including Pielou's evenness index, proportion of Paenibacillus, proportion of OTUs tolerant to organic pollution and proportion of Nitrosomonas. The results showed that the Ba-IBI was able to effectively discriminate different impaired site groups, and had a good correlation with the index of water quality (r = 0.79, p < 0.01) and the qualitative habitat evaluation index (r = 0.51, p < 0.01). Moreover, the Ba-IBI was negatively correlated with the number of population within a 1 km buffer (r = -0.71, p < 0.01). Application of the index showed that most of the sites were in the poor or bad class in the river. Our study revealed that the Ba-IBI is an effective and reliable approach for assessing the ecological status of Qinhuai River basin, which can complement the existing ecological assessment approaches for urban rivers. Meanwhile, repeted surveys and field validations are still needed to further improve the applicability of the index in future studies.

Determination of sediment metal background concentrations and enrichment in marine environments - A critical review

'Background' is the concentration of metals in pristine sediment, unaltered by human activity and 'enrichment' is the extent present-day sediment metal concentrations exceed pre-anthropogenic levels (the magnitude of human-induced change). Background and enrichment are becoming more frequently used for management measures to bring sediment and the environment back to near-pristine levels. Of the six empirical methods reviewed for determining background (global values, pristine marine and fluvial sediments, catchment soils and rocks), the use of sedimentary cores has the greatest advantage. Most of the eight statistical methods reviewed are adversely affected by the polymodality and an absence of normality or log-normality, however robust regression procedures are most commonly used. Sorption hypothesis techniques require further development. Indices used to determine enrichment incorporate background levels (enrichment indices) or do not (contamination indices). Of the 20 indices reviewed, the New Nemerow Index and the Mean Enrichment Quotient rate highly in performance, based on 5 beneficial attributes assessed: use of background and normalised data, provision of thresholds, a classification scheme, and inclusion of multiple metals. Variance in background metal concentrations determined in the 43 global projects reviewed is surprisingly moderate, however regional variability may be considerable due to local catchment mineralisation. Chemical analysis of sediment should not include metals bound in the mineral matrix and weak acid extractions are advisable. The use of appropriate and effective indicators of environmental condition are critical to the protection and restoration of marine regions and ensuring that human activities are carried out in a sustainable manner to promote safe, healthy and productive ecosystems.

A bacterial community-based index to assess the ecological status of estuarine and coastal environments

Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene amplicon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management.

A coastal three-dimensional water quality model of nitrogen in Jiaozhou Bay linking field experiments with modelling

With anthropogenic changes, the structure and quantity of nitrogen nutrients have changed in coastal ocean, which has dramatically influenced the water quality. Water quality modeling can contribute to the necessary scientific grounding of coastal management. In this paper, some of the dynamic functions and parameters of nitrogen were calibrated based on coastal field experiments covering the dynamic nitrogen processes in Jiaozhou Bay (JZB), including phytoplankton growth, respiration, and mortality; particulate nitrogen degradation; and dissolved organic nitrogen remineralization. The results of the field experiments and box model simulations showed good agreement (RSD=20%±2% and SI=0.77±0.04). A three-dimensional water quality model of nitrogen (3DWQMN) in JZB was improved and the dynamic parameters were updated according to field experiments. The 3DWQMN was validated based on observed data from 2012 to 2013, with good agreement (RSD=27±4%, SI=0.68±0.06, and K=0.48±0.04), which testifies to the model's credibility.

'The past is the future of the present': Learning from long-time series of marine monitoring

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.

Relationships between lines of evidence of pollution in estuarine areas: Linking contaminant levels with biomarker responses in mussels and with structure of macroinvertebrate benthic communities

Data obtained in a pollution survey performed in estuarine areas were integrated using multivariate statistics. The sites selected for the study were areas affected by treated and untreated urban discharges, harbours or industrial activities as well as reference sites. Mussels were transplanted to each site and after different times of exposure, samples of water, sediments and mussels were collected. Biomarkers were analysed on mussels after 3 and 21 days of transplant whereas concentrations of contaminants were measured in water, sediments and mussels after 21 days of transplant. The structure of macroinvertebrate benthic communities was studied in sediment samples. Studied variables were organised into 5 datasets, each one constituting a line of evidence (LOE): contaminants in water, contaminants in sediments, contaminants accumulated by transplanted mussels, biomarkers in transplanted mussels and changes in the structure of macroinvertebrate benthic communities of each sampling site. Principal Component Analysis (PCA) identified the variables of each LOE best explaining variability among sites. In order to know how LOEs relate to each other, Pearson's correlations were performed. Contaminants in sediments were not correlated with the rest of LOEs. Contaminants in water were significantly correlated with contaminants and biomarkers in mussels and with structure of macroinvertebrate benthic communities. Similarly, significant correlations were found between contaminants and biomarkers in mussels and between biomarkers in mussels and structure of macroinvertebrate benthic communities. In conclusion, biomarker responses give relevant information on pollution in estuarine areas and provide a link between chemical and ecological statuses of water bodies in the context of the Water Framework Directive.

Palaeo-ecological quality status based on foraminifera of Boulogne-sur-Mer harbour (Pas-de-Calais, Northeastern France) over the last 200 years

Over the last centuries, coastal areas have experienced dramatic degradations of their environmental quality, which has led to a huge reduction of marine biodiversity. The objective of the present study was to use geochemical parameters and benthic fossil foraminifera to assess environmental changes that have occurred over the last 200 years in a harbour area (Boulogne-sur-Mer, Northern France) heavily modified by human activities. A multidisciplinary approach including major and trace metals, grain-size, total organic carbon and benthic fossil foraminifera, has been performed on a 33-cm long core. The dating was carried out using the activity of (210)Pb and (137)Cs. Embayment of the area and increase of trace metals concentrations induced a shift in benthic communities. Human activities modified a sandy nearshore bank, colonized by typical marine foraminiferal species, such as Cribroelphiudium excavatum, into a sheltered environment, dominated by brackish end-members, such as Haynesina germanica. Along the sedimentary record, the interaction between meiofaunal and geochemical elements made it possible to distinguish between a pre-impacted period and an industrial period. The upper part of the core reflects better ecological conditions, indicating an environmental recovery. Our results provide baselines for future environmental bio-monitoring in the area.

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.

The mismatch of bioaccumulated trace metals (Cu, Pb and Zn) in field and transplanted oysters (Saccostrea glomerata) to ambient surficial sediments and suspended particulate matter in a highly urbanised estuary (Sydney estuary, Australia)

A significant correlation between sedimentary metals, particularly the 'bio-available' fraction, and bioaccumulated metal concentrations in the native Sydney rock oyster (Saccostrea glomerata) tissues has been successfully demonstrated previously for Cu and Zn in a number of estuaries in New South Wales, Australia. However, this relationship has been difficult to establish in a highly modified estuary (Sydney estuary, Australia) where metal contamination is of greatest concern and where a significant relationship would be most useful for environmental monitoring. The use of the Sydney rock oyster as a biomonitoring tool for metal contamination was assessed in the present study by investigating relationships between metals attached to sediments and suspended particulate matter (SPM) to bioaccumulated concentrations in oyster tissues. Surficial sediments (both total and fine-fraction), SPM and wild oysters were collected over 3 years from three embayments (Chowder Bay, Mosman Bay and Iron Cove) with each embayment representing a different physiographic region of Sydney estuary. In addition, a transplant experiment of farmed oysters was conducted in the same embayments for 3 months. No relationship was observed between sediments or SPM metals (Cu, Pb and Zn) to tissue of wild oysters; however, significant relationship was observed against transplanted oysters. The mismatch between wild and farmed, transplanted oysters is perplexing and indicates that wild oysters are unsuitable to be used as a biomonitoring tool due to the involvement of unknown complex factors while transplanted oysters hold strong potential.

Restoring fish ecological quality in estuaries: Implication of interactive and cumulative effects among anthropogenic stressors

Estuaries are subjected to multiple anthropogenic stressors, which have additive, antagonistic or synergistic effects. Current challenges include the use of large databases of biological monitoring surveys (e.g. the European Water Framework Directive) to help environmental managers prioritizing restoration measures. This study investigated the impact of nine stressor categories on the fish ecological status derived from 90 estuaries of the North East Atlantic countries. We used a random forest model to: 1) detect the dominant stressors and their non-linear effects; 2) evaluate the ecological benefits expected from reducing pressure from stressors; and 3) investigate the interactions among stressors. Results showed that largest restoration benefits were expected when mitigating water pollution and oxygen depletion. Non-additive effects represented half of pairwise interactions among stressors, and antagonisms were the most common. Dredged sediments, flow changes and oxygen depletion were predominantly implicated in non-additive interactions, whereas the remainder stressors often showed additive impacts. The prevalence of interactive impacts reflects a complex scenario for estuaries management; hence, we proposed a step-by-step restoration scheme focusing on the mitigation of stressors providing the maximum of restoration benefits under a multi-stress context.

A fish-based index for assessing the ecological status of Polish transitional and coastal waters

Fish assemblages are considered indicators of aquatic ecosystem quality. Based on how fish communities respond to anthropogenic pressures, we developed a multimetric fish index for evaluating the health of both coastal and transitional waters. Fish data were collected along the Polish coast in the years 2011, 2013 and 2014 using different types of gear. Redundancy analysis showed that the most important environmental factor affecting fish community was salinity. Responses to anthropogenic disturbances of 20 candidate metrics were tested by generalized linear models, taking into account salinity, sampling protocol and the proxy of human pressures described by the Baltic Sea Impact Index (BSII). Five selected metrics were combined in a Multimetric Index, which showed negative significant correlation with BSII. The index presented herein appeared to be a good tool for assessing the ecological state of highly impacted Polish transitional and coastal areas and complies with the Water Framework Directive requirements.

Dissecting the distribution of brittle stars along a sewage pollution gradient indicated by organic markers

We have assessed variation in brittle star distribution patterns along a contamination gradient identified by fecal steroids and aliphatic hydrocarbons in Paranaguá Bay, southern Brazil. A hierarchical design using multiple spatial scales (centimeters-kilometers) was applied. Generalized linear mixed models (GLMMs) were used to investigate the spatial and temporal variability of brittle stars. Main principal components from the contamination and environmental matrices were used to investigate the best explanatory dataset. The abundance of brittle stars was significantly lower in sites with high concentrations of fecal steroids and aliphatic hydrocarbons. The best model fitting always included components from the contamination gradients, which precludes a purely environmental driving of brittle star abundance. Variability in spatial scales lower than kilometers was probably driven by sediment characteristics. We highlighted the importance of a robust multi-scale sampling design for a better biological indication of coastal contamination.

Histopathological baseline levels and confounding factors in common sole (Solea solea) for marine environmental risk assessment

Liver and gonad histopathology, biometric parameters and hepatic metal bioaccumulation were assessed monthly over a one-year period in common soles from the Basque continental shelf, in order to determine baseline levels and confounding factors within biomonitoring studies. Biometric parameters and hepatic metal bioaccumulation varied according to season and gender. Accordingly, hepatic histopathological traits presented seasonal variations related to the reproductive cycle. However, the hepatic histopathological index showed that seasonality and gender were not significant confounding factors. Conversely, the gonad histopathological index was modulated by season and gender. As for organ comparison, the liver endured more severe histopathological damage than the gonad. In brief, the sampling period and gender may not affect the estimation of hepatic histopathological indices for biomonitoring purposes. Nonetheless, due to different sensitivities to environmental 'noise' variables, the sampling period and gender differentiation should be thoroughly considered for the assessment of gonad histopathology, biometrics and metal bioaccumulation.

Comprehensive assessment of coastal eutrophication in Taiwan and its implications for management strategy

Due to the rapid population growth, anthropogenic activities result in agricultural, industrial, and urban diffuse runoffs that elevate the level of nutrients such as nitrogen and phosphorus in coastal waters. Currently there is no integrated analysis for coastal eutrophication in Taiwan. A comprehensive analysis of the coastal eutrophic status was performed in this study based on decade-long coastal water quality monitoring data from Taiwan's Environmental Protection Administration. A 3-tiered monitoring strategy is recommended based on the severity of the current eutrophication state. Results indicate that the most problematic area of coastal eutrophication is located in the estuary of the Donggang River (DGR) and its adjacent coastal waters, i.e., the Kao-Ping mouth (KPM) and Dapeng Bay (DPB) in south-western Taiwan. With a worsening eutrophic status, these areas demand intensive monitoring and research with higher spatial and temporal resolutions to evaluate the stresses of nutrient forcing and predict possible future responses.

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.

A MSFD complementary approach for the assessment of pressures, knowledge and data gaps in Southern European Seas: The PERSEUS experience

PERSEUS project aims to identify the most relevant pressures exerted on the ecosystems of the Southern European Seas (SES), highlighting knowledge and data gaps that endanger the achievement of SES Good Environmental Status (GES) as mandated by the Marine Strategy Framework Directive (MSFD). A complementary approach has been adopted, by a meta-analysis of existing literature on pressure/impact/knowledge gaps summarized in tables related to the MSFD descriptors, discriminating open waters from coastal areas. A comparative assessment of the Initial Assessments (IAs) for five SES countries has been also independently performed. The comparison between meta-analysis results and IAs shows similarities for coastal areas only. Major knowledge gaps have been detected for the biodiversity, marine food web, marine litter and underwater noise descriptors. The meta-analysis also allowed the identification of additional research themes targeting research topics that are requested to the achievement of GES.

Wave Glider Monitoring of Sediment Transport and Dredge Plumes in a Shallow Marine Sandbank Environment

As human pressure on the marine environment increases, safeguarding healthy and productive seas increasingly necessitates integrated, time- and cost-effective environmental monitoring. Employment of a Wave Glider proved very useful for the study of sediment transport in a shallow sandbank area in the Belgian part of the North Sea. During 22 days, data on surface and water-column currents and turbidity were recorded along 39 loops around an aggregate-extraction site. Correlation with wave and tidal-amplitude data allowed the quantification of current- and wave-induced advection and resuspension, important background information to assess dredging impacts. Important anomalies in suspended particulate matter concentrations in the water column suggested dredging-induced overflow of sediments in the near field (i.e., dynamic plume), and settling of finer-grained material in the far field (i.e., passive plume). Capturing the latter is a successful outcome to this experiment, since the location of dispersion and settling of a passive plume is highly dependent on the ruling hydro-meteorological conditions and thus difficult to predict. Deposition of the observed sediment plumes may cause habitat changes in the long-term.

Developing an analytical framework for assessing progress toward ecosystem-based management

Ecosystem-based management (EBM) has become a key instrument of contemporary environmental policy and practice. Given the increasingly important role of EBM, there is an urgent need for improved analytical approaches to assess if and to what extent EBM has been accomplished in any given case. Drawing on the vast literature on EBM, we identify five key ecosystem aspects for assessment. By linking these aspects to four phases of management, we develop an interdisciplinary, analytical framework that enables a high-resolution and systematic assessment of the degree of specificity and integration of ecosystem aspects in an EBM. We then apply the framework to evaluate five coastal EBM initiatives in Sweden, four on the Baltic coast and one on the west coast. Our results demonstrate our framework's usefulness for in-depth and continuous assessments of processes aiming for EBM, and also provide an empirical basis for inferences about the key challenges for successful EBM.

Challenges and difficulties in assessing the environmental status under the requirements of the Ecosystem Approach in North African countries, illustrated by eutrophication assessment

Marine ecosystems provide many ecosystem goods and services. However, these ecosystems and the benefits they create for humans are subject to competing uses and increasing pressures. As a consequence of the increasing threats to the marine environment, several regulations require applying an ecosystem-based approach for managing the marine environment. Within the Mediterranean Sea, in 2008, the Contracting Parties of the Mediterranean Action Plan decided to progressively apply the Ecosystem Approach (EcAp) with the objective of achieving Good Environmental Status (GES) for 2018. To assess the environmental status, the EcAp proposes 11 Ecological Objectives, each of which requires a set of relevant indicators to be integrated. Progress towards the EcAp entails a gradual and important challenge for North African countries, and efforts have to be initiated to propose and discuss methods. Accordingly, to enhance the capacity of North African countries to implement EcAp and particularly to propose and discuss indicators and methods to assess GES, the aim of this manuscript is to identify the practical problems and gaps found at each stage of the environmental status assessment process. For this purpose, a stepwise method has been proposed to assess the environmental status using Ecologic Objective 5-Eutrophication as example.

A multi-molecular marker assessment of organic pollution in shore sediments from the Río de la Plata Estuary, SW Atlantic

Organic pollution was evaluated in surface sediments along the middle portion of the Río de la Plata Estuary, SW Atlantic. A multi-molecular marker approach was performed to identify major sources of organic compounds using diagnostic indices. The relative contribution of different sources of hydrocarbons was quantified by source apportionment employing Principal Component Analysis/Multiple Linear Regression (PCA/MLR) as chemometric technique. All molecular markers indicated high chronic organic pollution in the stations of Montevideo Bay. Main sources of aliphatic and polycyclic aromatic hydrocarbons were petroleum inputs and combustion, due to oil transport and refinement, harbour activities and vehicular emissions. Major sources of linear alkylbenzenes and steroids were industrial and domestic sewage. Although, significant anthropogenic inputs, a natural footprint of terrestrial higher plants contribution was recognized. Multi-molecular marker and comprehensive assessments can improve the establishment of more precise regulation actions to reduce pollution levels.

What does impacted look like? High diversity and abundance of epibiota in modified estuaries

Ecosystems modified by human activities are generally predicted to be biologically impoverished. However, much pollution impact theory stems from laboratory or small-scale field studies, and few studies replicate at the level of estuary. Furthermore, assessments are often based on sediment contamination and infauna, and impacts to epibiota (sessile invertebrates and algae) are seldom considered. We surveyed epibiota in six estuaries in south-east Australia. Half the estuaries were relatively pristine, and half were subject to internationally high levels of contamination, urbanisation, and industrialisation. Contrary to predictions, epibiota in modified estuaries had greater coverage and were similarly diverse as those in unmodified estuaries. Change in epibiota community structure was linearly correlated with sediment-bound copper, and the tubeworm Hydroides elegans showed a strong positive correlation with sediment metals. Stressors such as metal contamination can reduce biodiversity and productivity, but others such as nutrient enrichment and resource provision may obscure signals of impact.

Regional status assessment of stony corals in the US Virgin Islands

States may protect coral reefs using biological water quality standards outlined by the Clean Water Act. This requires biological assessments with indicators sensitive to human disturbance and regional, probability-based survey designs. Stony coral condition was characterized on a regional scale for the first time in the nearshore waters of the US Virgin Islands (USVI). Coral composition, abundance, size, and health were assessed at 66 stations in the St. Croix region in fall 2007 and at 63 stations in the St. Thomas and St. John region in winter 2009. Indicators were chosen for their sensitivity to human disturbance. Both surveys were probability-based (random) designs with station locations preselected from areas covered by hardbottom and coral reef substrate. Taxa richness was as high as 21 species but more than half the area of both regions exhibited taxa richness of <10 species in the 25 m(2) transect area. Coral density was as high as 5 colonies m(-2) but more than half the area of both regions had <2 colonies m(-2). Both regions showed similar dominant species based on frequency of occurrence and relative abundance. Because of large colony sizes, Montastrea annularis provided more total surface area and live surface area than more abundant species. The surveys establish baseline regional conditions and provide a foundation for long-term regional monitoring envisioned by the USVI Department of Planning and Natural Resources. The probabilistic sampling design assures the data can be used in Clean Water Act reporting.

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.

Integrated assessment of metal contamination in sediments from two tropical estuaries

In order to evaluate if sediment metal contamination is responsible for benthic degradation and identify possible reference sites in Todos os Santos Bay (TSB), comparisons between a highly impacted (Subaé) and less impacted (Jaguaripe) estuarine systems were made based on (i) field assessment of macrobenthic assemblage, (ii) sediment metal concentrations and (iii) chronic toxicity test with the tropical copepod Nitokra sp. Data were integrated by multivariate analysis (BIOENV and PCA) and the ratio-to-mean (RTMe) approach. Estuaries were divided into four different salinity zones to avoid misclassification of benthic conditions. Salinity was the main variable correlated to the benthic distribution in both estuaries, indicating that categories based on salinity features seem to be suitable in TSB. Correspondence among lines of evidence differed in low and high metal contaminated systems. Chronic toxicity was found along both the entire systems, being considerably higher in Jaguaripe. However, there was no clear evidence of metal contamination and benthic alteration in most stations of Jaguaripe. Although the concentrations of Sr and Cu were correlated to the benthic assemblage in Jaguaripe, it is unlikely that toxicity has been caused by these elements. The benthic assemblage distribution of Jaguaripe seems to be rather related to natural stressful conditions of transitional waters. Even though the Jaguaripe estuary might not be pristine, it can be used as a reference estuary for benthic assessment in TSB. Regarding the Subaé estuary, toxicity and Zn were also correlated to the benthic assemblage and most stations showed signs of benthic alteration and metal contamination. All lines of evidence were in agreement providing evidences that metal contamination might be responsible for benthic degradation in Subaé.

Towards a predictive model to assess the natural position of the Posidonia oceanica seagrass meadows upper limit

The upper portion of the meadows of the protected Mediterranean seagrass Posidonia oceanica occurs in the region of the seafloor mostly affected by surf-related effects. Evaluation of its status is part of monitoring programs, but proper conclusions are difficult to draw due to the lack of definite reference conditions. Comparing the position of the meadow upper limit with the beach morphodynamics (i.e. the distinctive type of beach produced by topography and wave climate) provided evidence that the natural landwards extension of meadows can be predicted. An innovative model was therefore developed in order to locate the region of the seafloor where the meadow upper limit should lie in natural conditions (i.e. those governed only by hydrodynamics, in absence of significant anthropogenic impact). This predictive model was validated in additional sites, which showed perfect agreement between predictions and observations. This makes the model a valuable tool for coastal management.

A biomarker of contaminant exposure is effective in large scale assessment of ten estuaries

Cost-effective and sensitive measures of anthropogenic stress are necessary tools in any environmental monitoring program. When implementing new monitoring tools in a region, rigorous laboratory and field studies are essential for characterizing the sensitivity and efficacy of the approach. We exposed the oyster Saccostrea glomerata to various individual contaminants through multiple exposure pathways (water- and food-borne) in the laboratory and measured two biomarker responses, lysosomal membrane stability (LMS) and lipid peroxidation (LPO). LMS was sensitive to both contaminant exposure pathways. We subsequently measured this biomarker in oysters which had been experimentally deployed at multiple sites in each of ten estuaries with varying levels of contamination associated with re-suspended sediments. There was a strong association between LMS and metal exposure, despite substantial natural variation in water quality parameters. Our results illustrate the potential use of LMS as a pragmatic indicator of biotic injury in environmental monitoring programs for re-suspended contaminated sediments.

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.