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

Hydroacoustics as a tool to examine the effects of Marine Protected Areas and habitat type on marine fish communities

Hydroacoustic technologies are widely used in fisheries research but few studies have used them to examine the effects of Marine Protected Areas (MPAs). We evaluate the efficacy of hydroacoustics to examine the effects of closure to fishing and habitat type on fish populations in the Cabo Pulmo National Park (CPNP), Mexico, and compare these methods to Underwater Visual Censuses (UVC). Fish density, biomass and size were all significantly higher inside the CPNP (299%, 144% and 52% respectively) than outside in non-MPA control areas. These values were much higher when only accounting for the reefs within the CPNP (4715%, 6970% and 97% respectively) highlighting the importance of both habitat complexity and protection from fishing for fish populations. Acoustic estimates of fish biomass over reef-specific sites did not differ significantly from those estimated using UVC data, although acoustic densities were less due to higher numbers of small fish recorded by UVC. There is thus considerable merit in nesting UVC surveys, also providing species information, within hydroacoustic surveys. This study is a valuable starting point in demonstrating the utility of hydroacoustics to assess the effects of coastal MPAs on fish populations, something that has been underutilised in MPA design, formation and management.

The relationship between observational scale and explained variance in benthic communities

This study addresses the impact of spatial scale on explaining variance in benthic communities. In particular, the analysis estimated the fraction of community variation that occurred at a spatial scale smaller than the sampling interval (i.e., the geographic distance between samples). This estimate is important because it sets a limit on the amount of community variation that can be explained based on the spatial configuration of a study area and sampling design. Six benthic data sets were examined that consisted of faunal abundances, common environmental variables (water depth, grain size, and surficial percent cover), and sonar backscatter treated as a habitat proxy (categorical acoustic provinces). Redundancy analysis was coupled with spatial variograms generated by multiscale ordination to quantify the explained and residual variance at different spatial scales and within and between acoustic provinces. The amount of community variation below the sampling interval of the surveys (< 100 m) was estimated to be 36-59% of the total. Once adjusted for this small-scale variation, > 71% of the remaining variance was explained by the environmental and province variables. Furthermore, these variables effectively explained the spatial structure present in the infaunal community. Overall, no scale problems remained to compromise inferences, and unexplained infaunal community variation had no apparent spatial structure within the observational scale of the surveys (> 100 m), although small-scale gradients (< 100 m) below the observational scale may be present.

BENFES, a new biotic index for assessing ecological status of soft-bottom communities. Towards a lower taxonomic complexity, greater reliability and less effort

The new biotic index BENFES (Benthic Families Ecological Status Index) for assessing the ecological status of soft-bottom communities based on presence/absence at the taxonomic family level, is described. BENFES was primarily developed for the communities from the Guadalquivir estuary (South-western Spain), but the aim of the present work was to evaluate the reliability and validity of this index for its application in the Water Framework Directive (WFD), especially as a preliminary and rapid assessment method for monitoring the ecological status of transitional and coastal waters. BENFES was compared with five widely used indices (BOPA, BO2A, BENTIX; AMBI and M-AMBI) in several studies from Southwestern Spain. In addition, we have also established comparisons between these indices and the most commonly used Shannon-Wiener diversity. M-AMBI and BENFES showed the best agreement in ecological status assignation and were the most useful and discriminant between the studied areas. BENTIX was a good discriminant in coastal areas but was severe with the environmental condition from estuaries; BOPA/BO2A did not show clear trends in most of the zones; and AMBI tended to provide overestimations of the ecological status. In conclusion, BENFES shows several advantages such as lower taxonomic resolution, greater reliability and only requiring presence/absence. All this implies a huge possibility to perform a simplified monitoring routine for the control of the ecological quality of water bodies.

A dual indicator approach for monitoring benthic impacts from organic enrichment with test application near Atlantic salmon farms

The organic enrichment of surficial sediments has a known effect on benthic faunal communities due largely to oxygen depletion and sulfide toxicity. Total dissolved sulfide (free S^-2=H₂S+HS^-+S^2-) concentrations in sediments are widely measured as a practical indicator of community effects. However, the standard ion selective electrode (ISE) method for free S^-2 analysis can provide biased results owing to the inclusion of non-toxic mineral sulfides and the oxidation and volatilization of free S^-2. A rapid field protocol was developed that alleviates these problems while also providing data on dissolved oxygen concentrations. Sediments collected near salmon aquaculture pens over cohesive and permeable substrates were analysed using the standard and new protocols. The results confirm previous conclusions of artifacts with the standard ISE method, while the dual indicator approach more accurately describes the stages, spatial extent and magnitude of sediment geochemical alterations affecting benthic communities.

Baseline evaluation of sediment contamination in the shallow coastal areas of Saudi Arabian Red Sea

Despite the growing recognition of the importance of water and sediment quality there is still limited information on contamination levels in many regions globally including the Red Sea. This study provides a comprehensive assessment of three classes of contaminants (Polycyclic Aromatic Hydrocarbons - PAH; metals; plastics) in coastal sediments along the Saudi Arabian Red Sea mainly collected using grabs. Background concentrations are provided for metals in the region. Concentrations of metals and PAH were generally low in comparison to international guidelines. A clear relationship between the concentration of metals and anthropogenic sources was not always apparent and dust and vegetation may be relevant players in the region. Microplastic items (mainly polyethylene) were abundant (reaching up to 1gm^-2 and 160piecesm^-2) and in general associated with areas of high human activity. This study provides critical information for future monitoring and the development of national policies within the Red Sea region.

Integration of community structure data reveals observable effects below sediment guideline thresholds in a large estuary

The sustainable management of estuarine and coastal ecosystems requires robust frameworks due to the presence of multiple physical and chemical stressors. In this study, we assessed whether ecological health decline, based on community structure composition changes along a pollution gradient, occurred at levels below guideline threshold values for copper, zinc and lead. Canonical analysis of principal coordinates (CAP) was used to characterise benthic communities along a metal contamination gradient. The analysis revealed changes in benthic community distribution at levels below the individual guideline values for the three metals. These results suggest that field-based measures of ecological health analysed with multivariate tools can provide additional information to single metal guideline threshold values to monitor large systems exposed to multiple stressors.

Sediment quality benchmarks for assessing oil-related impacts to the deep-sea benthos

Paired sediment contaminant and benthic infaunal data from prior studies following the 2010 Deepwater Horizon (DWH) oil spill in the Gulf of Mexico were analyzed using logistic regression models (LRMs) to derive sediment quality benchmarks for assessing risks of oil-related impacts to the deep-sea benthos. Sediment total polycyclic aromatic hydrocarbon (PAH) and total petroleum hydrocarbon (TPH) concentrations were used as measures of oil exposure. Taxonomic richness (average number of taxa/sample) was selected as the primary benthic response variable. Data are from 37 stations (1300-1700 m water depth) in fine-grained sediments (92%-99% silt-clay) sampled within 200 km of the DWH wellhead (most within 40 km) in 2010 and 32 stations sampled in 2011 (29 of which were common to both years). Results suggest the likelihood of impacts to benthic macrofauna and meiofauna communities is low (<20%) at TPH concentrations of less than 606 mg kg^-1 (ppm dry weight) and 700 mg kg^-1 respectively, high (>80%) at concentrations greater than 2144 mg kg^-1 and 2359 mg kg^-1 respectively, and intermediate at concentrations in between. For total PAHs, the probability of impacts is low (<20%) at concentrations of less than 4.0 mg kg^-1 (ppm) for both macrofauna and meiofauna, high (>80%) at concentrations greater than 24 mg kg^-1 and 25 mg kg^-1 for macrofauna and meiofauna, respectively, and intermediate at concentrations in between. Although numerical sediment quality guidelines (SQGs) are available for total PAHs and other chemical contaminants based on bioeffect data for shallower estuarine, marine, and freshwater biota, to our knowledge, none have been developed for measures of total oil (e.g., TPH) or specifically for deep-sea benthic applications. The benchmarks presented herein provide valuable screening tools for evaluating the biological significance of observed oil concentrations in similar deep-sea sediments following future spills and as potential restoration targets to aid in managing recovery. Integr Environ Assess Manag 2017;13:840-851. Published 2017. This article is a US Government work and is in the public domain in the USA.

Analysis of macrobenthic assemblages and ecological health of Yellow River Delta, China, using AMBI & M-AMBI assessment method

Yellow River delta (YRD) is a typical example of a valuable coastal ecosystem that is under increasing anthropogenic threat in China. To understand the current health status of this region, three surveys in 2011 for the abiotic conditions and macrobenthic assemblages were performed. The concentration of trace metals were relatively low in the sediment at all sampling stations representing a good sediment quality. A total of 159 macrobenthic species were identified during the three surveys. ABC curves showed that the macrobenthic fauna at 8 sampling stations suffered disturbances from human activities. M-AMBI index indicates that the benthic ecological quality of YRD is currently still not in a good condition. Five trace metals, water temperature and depth were the main environmental variables affecting the distribution pattern of macrobenthic assemblages. Community succession has occurred over the past 60years, as evidenced by changes of species composition, key species, distribution pattern and range.

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments

Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a “sufficient” replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.

An ecosystem-based approach to assess the status of Mediterranean algae-dominated shallow rocky reefs

A conceptual model was constructed for the functioning the algae-dominated rocky reef ecosystem of the Mediterranean Sea. The Ecosystem-Based Quality Index (reef-EBQI) is based upon this model. This index meets the objectives of the EU Marine Strategy Framework Directive. It is based upon (i) the weighting of each compartment, according to its importance in the functioning of the ecosystem; (ii) biological parameters assessing the state of each compartment; (iii) the aggregation of these parameters, assessing the quality of the ecosystem functioning, for each site; (iv) and a Confidence Index measuring the reliability of the index, for each site. The reef-EBQI was used at 40 sites in the northwestern Mediterranean. It constitutes an efficient tool, because it is based upon a wide set of functional compartments, rather than upon just a few species; it is easy and inexpensive to implement, robust and not redundant with regard to already existing indices.

Assessing environmental health using ecological indices for soft bottom in sewage-affected rocky shores: The case of the largest seaside resort of SW Atlantic

Efficient ecological indices can reflect the differences between impacted and nonimpacted sites, leading to significant variations at the contamination spatial scale. Here, we evaluated the spatial-temporal variability of 3 ecological indices (AMBI, M-AMBI, and BENTIX) in response to the distinct levels of sewage contamination. The indices were evaluated in two different ways: including Brachidontes rodriguezii (IBR) and excluding B. rodriguezii (EBR). The fact that mussel beds create a secondary infaunal habitat allows us to test these indices for soft bottoms in areas with rocky bottoms. The effectiveness and the level of agreement of these indices were increased when they were calculated with EBR. BENTIX and M-AMBI produced under- and overestimations of the ecological status of the studied sites. AMBI (EBR) seems to be better suited for environmental quality assessment in the study area. This index reduces the processing time of samples; thus, the AMBI (EBR) index could be used as a robust management tool for monitoring programs in areas with hard substrate.

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.

Structure and biodiversity of coralligenous assemblages dominated by the precious red coral Corallium rubrum over broad spatial scales

Data on species diversity and structure in coralligenous outcrops dominated by Corallium rubrum are lacking. A hierarchical sampling including 3 localities and 9 sites covering more than 400 km of rocky coasts in NW Mediterranean, was designed to characterize the spatial variability of structure, composition and diversity of perennial species inhabiting coralligenous outcrops. We estimated species/taxa composition and abundance. Eight morpho-functional groups were defined according to their life span and growth to characterize the structural complexity of the outcrops. The species composition and structural complexity differed consistently across all spatial scales considered. The lowest and the highest variability were found among localities (separated by >200 km) and within sites (separated by 1–5 km), respectively supporting differences in diversity indices. The morpho-functional groups displayed a consistent spatial arrangement in terms of the number, size and shape of patches across study sites. These results contribute to filling the gap on the understanding of assemblage composition and structure and to build baselines to assess the response of this of this highly threatened habitat to anthropogenic disturbances.

Four Reasons to Question the Accuracy of a Biotic Index; the Risk of Metric Bias and the Scope to Improve Accuracy

Natural ecological variability and analytical design can bias the derived value of a biotic index through the variable influence of indicator body-size, abundance, richness, and ascribed tolerance scores. Descriptive statistics highlight this risk for 26 aquatic indicator systems; detailed analysis is provided for contrasting weighted-average indices applying the example of the BMWP, which has the best supporting data. Differences in body size between taxa from respective tolerance classes is a common feature of indicator systems; in some it represents a trend ranging from comparatively small pollution tolerant to larger intolerant organisms. Under this scenario, the propensity to collect a greater proportion of smaller organisms is associated with negative bias however, positive bias may occur when equipment (e.g. mesh-size) selectively samples larger organisms. Biotic indices are often derived from systems where indicator taxa are unevenly distributed along the gradient of tolerance classes. Such skews in indicator richness can distort index values in the direction of taxonomically rich indicator classes with the subsequent degree of bias related to the treatment of abundance data. The misclassification of indicator taxa causes bias that varies with the magnitude of the misclassification, the relative abundance of misclassified taxa and the treatment of abundance data. These artifacts of assessment design can compromise the ability to monitor biological quality. The statistical treatment of abundance data and the manipulation of indicator assignment and class richness can be used to improve index accuracy. While advances in methods of data collection (i.e. DNA barcoding) may facilitate improvement, the scope to reduce systematic bias is ultimately limited to a strategy of optimal compromise. The shortfall in accuracy must be addressed by statistical pragmatism. At any particular site, the net bias is a probabilistic function of the sample data, resulting in an error variance around an average deviation. Following standardized protocols and assigning precise reference conditions, the error variance of their comparative ratio (test-site:reference) can be measured and used to estimate the accuracy of the resultant assessment.

Monitoring the effects of wastewater treatment strategies

Wastewater disposal in coastal waters causes widespread environmental problems. Secondary treatment is expected to reduce the adverse effects of insufficiently treated wastewater. The environmental impact of sewage disposal via 18 wastewater treatment plants was analysed using the benthic opportunistic polychaetes and amphipods (BOPA) index. In previous studies this index proved to be an effective tool for monitoring sewage pollution. The impact of these discharges was highly related to treatment level, which ranged from pre-treatment to biological, as well as to flow rates and outfall position. Locations affected by pre-treated wastewater showed environmental degradation, especially marked near outfalls with higher flow rates. At most locations, biologically treated wastewater did not cause a significant impact and an improvement in ecological integrity was detected after this secondary treatment had been implemented. The impact of discharge was highly related to chemical oxygen demand (COD), suspended solids and nutrient concentrations, which are all lower in biologically treated wastewater. A 'moderate' ecological status was observed not only near sewage outfalls with high wastewater flow rates (>1,500,000 m(3)/month) with a COD over 200 mg/l but also near those with lower flow rates but with a COD over 400 mg/l. To reduce the impact of sewage disposal, it is necessary to carry out adequate treatment, have site outfalls deep enough, and implement water recycling.

Performance evaluation and validation of ecological indices toward site-specific application for varying benthic conditions in Korean coasts

Although several ecological indices have been developed worldwide to assess the ecological quality (EcoQ) status of coastal environments, their applicability remains in question. The present study evaluated the performance of 14 univariate and multivariate indices selected to provide a good description of benthic EcoQ status. We specifically investigated on i) spatial and regional variability, ii) (dis)similarity between ecological indices, and iii) the association of selected indices against heavy metal pollution. Benthic community data were collected from six coastal regions of Korea (n=365) that have varying land-use activity in adjacent inland areas (municipal, industrial, and rural). Abiotic sedimentary parameters were also considered as possible pressures associated with benthic community responses, including grain size, organic carbon content, and heavy metal pollution. The macrozoobenthic biodiversity and EcoQ results generally well reflected the geographical settings and the pollution gradient of heavy metals between regions. Among the six selected indices (H', AMBI, BPI, BQI, EQR, and M-AMBI), BPI appeared to be the most tolerant index, with >90% of locations being classified as "High" to "Good" while EQR showed the clear classification across the EcoQ status range. Significant disagreement between BQI vs. AMBI, BPI vs. M-AMBI, and AMBI vs. M-AMBI were found. Overall, single or limited indices seemed to over- or underestimate the given benthic conditions, warranting the use of site-specific indices at specific areas and/or locations. In conclusion, our study demonstrates the utility of applying different ecological or multivariate indices to infer the general ecological status of specific sites to gauge the extent of sedimentary pollution.

Response of benthos to ocean outfall discharges: does a general pattern exist?

We assessed the effects of 40 ocean outfalls on adjacent macrobenthic invertebrates. Data were obtained from a review of gray and peer-review literature. Different parameters describing the outfall characteristics were compiled (length, maximum depth, treatment level, flow and organic matter mass discharged). Exposure to wave action was represented by significant wave height. The magnitude of the effect was categorized in three impact levels and classified considering different ecological indicators. A theoretical predictive model was formulated in which the lower the organic matter and the higher the energy of the system, the lower the benthic impact. The main conclusion was that the general pattern of the succession of benthic communities brought about by ocean outfalls fits the model of Pearson-Rosenberg but with some deviations i) the probability of a significant impact is much lower, ii) not all the successional stages occur and, iii) the magnitude of the changes are usually lower.

Environmental and anthropogenic factors affecting the probability of occurrence of Oncomegas wageneri (Cestoda: Trypanorhyncha) in the southern Gulf of Mexico

Background

Understanding the environmental and anthropogenic factors influencing the probability of occurrence of the marine parasitic species is fundamental for determining the circumstances under which they can act as bioindicators of environmental impact. The aim of this study was to determine whether physicochemical variables, polyaromatic hydrocarbons or sewage discharge affect the probability of occurrence of the larval cestode Oncomegas wageneri, which infects the shoal flounder, Syacium gunteri, in the southern Gulf of Mexico.

Methods

The study area included 162 sampling sites in the southern Gulf of Mexico and covered 288,205 km², where the benthic sediments, water and the shoal flounder individuals were collected. We used the boosted generalised additive models (boosted GAM) and the MaxEnt to examine the potential statistical relationships between the environmental variables (nutrients, contaminants and physicochemical variables from the water and sediments) and the probability of the occurrence of this parasite. The models were calibrated using all of the sampling sites (full area) with and without parasite occurrences (n = 162) and a polygon area that included sampling sites with a depth of 1500 m or less (n = 134).

Results

Oncomegas wageneri occurred at 29/162 sampling sites. The boosted GAM for the full area and the polygon area accurately predicted the probability of the occurrence of O. wageneri in the study area. By contrast, poor probabilities of occurrence were obtained with the MaxEnt models for the same areas. The variables with the highest frequencies of appearance in the models (proxies for the explained variability) were the polyaromatic hydrocarbons of high molecular weight (PAHH, 95 %), followed by a combination of nutrients, spatial variables and polyaromatic hydrocarbons of low molecular weight (PAHL, 5 %).

Conclusions

The contribution of the PAHH to the variability was explained by the fact that these compounds, together with N and P, are carried by rivers that discharge into the ocean, which enhances the growth of hydrocarbonoclastic bacteria and the productivity and number of the intermediate hosts. Our results suggest that sites with PAHL/PAHH ratio values up to 1.89 promote transmission based on the high values of the prevalence of O. wageneri in the study area. In contrast, PAHL/PAHH ratio values ≥ 1.90 can be considered harmful for the transmission stages of O. wageneri and its hosts (copepods, shrimps and shoal flounders). Overall, the results indicate that the PAHHs affect the probability of occurrence of this helminth parasite in the southern Gulf of Mexico.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-1222-6) contains supplementary material, which is available to authorized users.

Calcareous Bio-Concretions in the Northern Adriatic Sea: Habitat Types, Environmental Factors that Influence Habitat Distributions, and Predictive Modeling

Habitat classifications provide guidelines for mapping and comparing marine resources across geographic regions. Calcareous bio-concretions and their associated biota have not been exhaustively categorized. Furthermore, for management and conservation purposes, species and habitat mapping is critical. Recently, several developments have occurred in the field of predictive habitat modeling, and multiple methods are available. In this study, we defined the habitats constituting northern Adriatic biogenic reefs and created a predictive habitat distribution model. We used an updated dataset of the epibenthic assemblages to define the habitats, which we verified using the fuzzy k-means (FKM) clustering method. Redundancy analysis was employed to model the relationships between the environmental descriptors and the FKM membership grades. Predictive modelling was carried out to map habitats across the basin. Habitat A (opportunistic macroalgae, encrusting Porifera, bioeroders) characterizes reefs closest to the coastline, which are affected by coastal currents and river inputs. Habitat B is distinguished by massive Porifera, erect Tunicata, and non-calcareous encrusting algae (Peyssonnelia spp.). Habitat C (non-articulated coralline, Polycitor adriaticus) is predicted in deeper areas. The onshore-offshore gradient explains the variability of the assemblages because of the influence of coastal freshwater, which is the main driver of nutrient dynamics. This model supports the interpretation of Habitat A and C as the extremes of a gradient that characterizes the epibenthic assemblages, while Habitat B demonstrates intermediate characteristics. Areas of transition are a natural feature of the marine environment and may include a mixture of habitats and species. The habitats proposed are easy to identify in the field, are related to different environmental features, and may be suitable for application in studies focused on other geographic areas. The habitat model outputs provide insight into the environmental drivers that control the distribution of the habitat and can be used to guide future research efforts and cost-effective management and conservation plans.

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.

Effect of thematic map misclassification on landscape multi-metric assessment

Advancements in remote sensing and computational tools have increased our awareness of large-scale environmental problems, thereby creating a need for monitoring, assessment, and management at these scales. Over the last decade, several watershed and regional multi-metric indices have been developed to assist decision-makers with planning actions of these scales. However, these tools use remote-sensing products that are subject to land-cover misclassification, and these errors are rarely incorporated in the assessment results. Here, we examined the sensitivity of a landscape-scale multi-metric index (MMI) to error from thematic land-cover misclassification and the implications of this uncertainty for resource management decisions. Through a case study, we used a simplified floodplain MMI assessment tool, whose metrics were derived from Landsat thematic maps, to initially provide results that were naive to thematic misclassification error. Using a Monte Carlo simulation model, we then incorporated map misclassification error into our MMI, resulting in four important conclusions: (1) each metric had a different sensitivity to error; (2) within each metric, the bias between the error-naive metric scores and simulated scores that incorporate potential error varied in magnitude and direction depending on the underlying land cover at each assessment site; (3) collectively, when the metrics were combined into a multi-metric index, the effects were attenuated; and (4) the index bias indicated that our naive assessment model may overestimate floodplain condition of sites with limited human impacts and, to a lesser extent, either over- or underestimated floodplain condition of sites with mixed land use.

Calculation of species sensitivity values and their precision in marine benthic faunal quality indices

A challenging aspect of benthic quality indices used for assessing the marine environment has been to compile reliable measures of the species' sensitivity to disturbances. Sensitivity values and their uncertainties can be calculated, but a problem to cope with is that the results may depend on the actual proportion of samples from disturbed and undisturbed environments. Here we calculated sensitivity values for each species along an artificial disturbance gradient created by bootstrapping varying numbers of samples from disturbed and undisturbed environments. The values were increasing, decreasing, or more or less constant along this gradient. The lowest value with the lowest uncertainty was adopted as the species sensitivity value. Analyses of the uncertainties indicated that the accuracy rather than the precision might be a concern. We suggest a method to exclude species for which the uncertainty is outside predefined limits as a precaution to reduce bias in the environmental status classification.

Knowledge of Brazilian benthic marine fauna throughout time

The ecosystems of Brazil's continental shelf and oceanic islands comprise a variety of environments that display unique geomorphological and geophysical features and biotic components. The quest to attain knowledge of Brazilian marine fauna is hampered by coastline length, biodiversity, a high rate of endemism, and a shortage of specialized researchers. Based on a systematic bibliographic review, the article offers an overview of the history, current knowledge, and outlook for the field of marine biodiversity in Brazil. Our findings show that government initiatives have afforded greater knowledge of Brazilian marine fauna species and opened new perspectives, including reliance on complex tools to describe benthic marine habitats in terms of their geological, geophysical, and biotic composition.

An ecosystem-based approach to assess the status of a Mediterranean ecosystem, the Posidonia oceanica seagrass meadow

Biotic indices, which reflect the quality of the environment, are widely used in the marine realm. Sometimes, key species or ecosystem engineers are selected for this purpose. This is the case of the Mediterranean seagrass Posidonia oceanica, widely used as a biological quality element in the context of the European Union Water Framework Directive (WFD). The good quality of a water body and the apparent health of a species, whether or not an ecosystem engineer such as P. oceanica, is not always indicative of the good structure and functioning of the whole ecosystem. A key point of the recent Marine Strategy Framework Directive (MSFD) is the ecosystem-based approach. Here, on the basis of a simplified conceptual model of the P. oceanica ecosystem, we have proposed an ecosystem-based index of the quality of its functioning, compliant with the MSFD requirements. This index (EBQI) is based upon a set of representative functional compartments, the weighting of these compartments and the assessment of the quality of each compartment by comparison of a supposed baseline. The index well discriminated 17 sites in the north-western Mediterranean (French Riviera, Provence, Corsica, Catalonia and Balearic Islands) covering a wide range of human pressure levels. The strong points of the EBQI are that it is easy to implement, non-destructive, relatively robust, according to the selection of the compartments and to their weighting, and associated with confidence indices that indicate possible weakness and biases and therefore the need for further field data acquisition.

Environmental status assessment using DNA metabarcoding: towards a genetics based Marine Biotic Index (gAMBI)

Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to be evaluated. Here, we analyze the requirements for the implementation of a genetics based AMBI (gAMBI), and show, using available sequence data, that information about presence/absence of the most frequently occurring species provides accurate AMBI values. Our results set the basics for the implementation of the gAMBI, which has direct implications for a faster and cheaper marine monitoring and health status assessment.

Verifying a biotope classification using benthic communities--an analysis towards the implementation of the European Marine Strategy Framework Directive

The HELCOM Red List biotopes project proposed a Baltic Sea wide classification consisting of six levels: The HELCOM Underwater biotopes/habitats classification system (HELCOM HUB). We present a case study from the south-western Baltic Sea where we tested the applicability of this system. More than 500 sampling stations were analyzed regarding macrozoobenthic communities and their linkage to environmental parameters. Based on the analyses of biotic and abiotic data, 21 groups were assigned to 13 biotopes of the classification. For some biotopes varying states of communities were recognized. Even though not all abiotic parameters are considered directly in the hierarchy of the classification in general, all soft-bottom communities could be allocated to a corresponding biotope. The application of the HELCOM HUB for the south-western Baltic Sea is feasible, in regard to the implementation of the European Marine Strategy Framework Directive as well as the Baltic Sea Action Plan.

Do contaminants originating from state-of-the-art treated wastewater impact the ecological quality of surface waters?

Since the 1980s, advances in wastewater treatment technology have led to considerably improved surface water quality in the urban areas of many high income countries. However, trace concentrations of organic wastewater-associated contaminants may still pose a key environmental hazard impairing the ecological quality of surface waters. To identify key impact factors, we analyzed the effects of a wide range of anthropogenic and environmental variables on the aquatic macroinvertebrate community. We assessed ecological water quality at 26 sampling sites in four urban German lowland river systems with a 0–100% load of state-of-the-art biological activated sludge treated wastewater. The chemical analysis suite comprised 12 organic contaminants (five phosphor organic flame retardants, two musk fragrances, bisphenol A, nonylphenol, octylphenol, diethyltoluamide, terbutryn), 16 polycyclic aromatic hydrocarbons, and 12 heavy metals. Non-metric multidimensional scaling identified organic contaminants that are mainly wastewater-associated (i.e., phosphor organic flame retardants, musk fragrances, and diethyltoluamide) as a major impact variable on macroinvertebrate species composition. The structural degradation of streams was also identified as a significant factor. Multiple linear regression models revealed a significant impact of organic contaminants on invertebrate populations, in particular on Ephemeroptera, Plecoptera, and Trichoptera species. Spearman rank correlation analyses confirmed wastewater-associated organic contaminants as the most significant variable negatively impacting the biodiversity of sensitive macroinvertebrate species. In addition to increased aquatic pollution with organic contaminants, a greater wastewater fraction was accompanied by a slight decrease in oxygen concentration and an increase in salinity. This study highlights the importance of reducing the wastewater-associated impact on surface waters. For aquatic ecosystems in urban areas this would lead to: (i) improvement of the ecological integrity, (ii) reduction of biodiversity loss, and (iii) faster achievement of objectives of legislative requirements, e.g., the European Water Framework Directive.

Classification of the ecological quality of the Aysen and Baker Fjords (Patagonia, Chile) using biotic indices

The AZTI's marine biotic index (AMBI), an ecological indicator for managing estuarine and coastal waters worldwide, was tested in two fjords in Chilean Patagonia. The Aysen Fjord (42° Lat. S) supports intensive salmon farming in coastal ecosystems, while the Baker Fjord (48° Lat. S) is currently just beyond the limit of the southern expansion of salmon concessions. The ecological status of the Aysen Fjord was classified as good, while the status of the Baker Fjord was classified as high and unbalanced. These differences were consistent with our expectations, illustrating the effect of local environmental conditions and human activities, combined with river inputs into semi-confined fjords. This method is appropriate for the evaluation of the ecological status of the fjords, but requires a sufficient amount of data for the robust environmental assessment as proposed by the Water Framework Directive (WFD).

Traditional Ecological Knowledge and the mapping of benthic marine habitats

Traditional Ecological Knowledge (TEK) is the empirically accumulated knowledge of local communities whose livelihoods depend directly on natural resources. TEK has a considerable potential as a reliable, rapid and low cost information source. However, its use for decision making in environmental management is frequently challenged due to the lack of scientific validation and the multiple and poorly understood biases deriving from measurement and analytical errors, as well as from political, cultural and religious sources. During the planning stage of a Marine Protected Area (MPA) in Southeastern Brazil we assessed fisherfolk TEK regarding seabed features, comparing it with results from a conventional oceanographic assessment. TEK was acquired and synthesized during a survey involving 19 fishing villages and a consensus analysis that minimized variation among individual fisherfolks and communities. The oceanographic survey included high resolution benthic habitat mapping tools such as sidescan sonar and ground-truthing with SCUBA near the interfaces of benthic features identified by fisherfolk. Nearly 3000 km(2) of seafloor were mapped by local fisherfolk as "gravel", "sand", "mud" and "reef structures", while side-scan sonar surveys covered approximately 360 km with an average 400 m swath. Analyses of overlap and proximity showed that TEK is relatively cost-effective and accurate for large-scale benthic surveys, especially as a starting point for planning oceanographic surveys. Moreover, including TEK in the planning stage of MPAs may increase communities' participation and understanding of the costs and benefits of the new access and fishing effort regulations.

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.

Effect of sample area and sieve size on benthic macrofaunal community condition assessments in California enclosed bays and estuaries

Benthic macrofauna are used extensively for environmental assessment, but the area sampled and sieve sizes used to capture animals often differ among studies. Here, we sampled 80 sites using 3 different sized sampling areas (0.1, 0.05, 0.0071 m(2)) and sieved those sediments through each of 2 screen sizes (0.5, 1 mm) to evaluate their effect on number of individuals, number of species, dominance, nonmetric multidimensional scaling (MDS) ordination, and benthic community condition indices that are used to assess sediment quality in California. Sample area had little effect on abundance but substantially affected numbers of species, which are not easily scaled to a standard area. Sieve size had a substantial effect on both measures, with the 1-mm screen capturing only 74% of the species and 68% of the individuals collected in the 0.5-mm screen. These differences, though, had little effect on the ability to differentiate samples along gradients in ordination space. Benthic indices generally ranked sample condition in the same order regardless of gear, although the absolute scoring of condition was affected by gear type. The largest differences in condition assessment were observed for the 0.0071-m(2) gear. Benthic indices based on numbers of species were more affected than those based on relative abundance, primarily because we were unable to scale species number to a common area as we did for abundance.

Macrobenthic community for assessment of estuarine health in tropical areas (Northeast, Brazil): review of macrofauna classification in ecological groups and application of AZTI Marine Biotic Index

The aim of the present study was to investigate the ecological quality of tropical estuaries on the northeastern coast of Brazil using the AMBI. Macrofauna classification based on ecological groups was reviewed using the Indicator Value (IndVal) coefficient. The results indicate that the ecosystems exhibit some level of disturbance. Most sites are situated between slightly-moderately disturbed boundaries due to the higher proportion of Nematoda (assigned here as Ecological Group I) and of Oligochaeta and Tubificidae (both classified as Ecological Group V). The AMBI proved efficient in evaluating environmental status, although the applicability of this index requires adjustments regarding some species in ecological groups. The present study also highlights the merits of the IndVal method for examining the assignments of species/taxa to an ecological group and demonstrates the validity of this coefficient is an assessment tool. Moreover, the complementary use of different methods is recommended for the assessment of ecosystem quality.

Performance of two Southern California benthic community condition indices using species abundance and presence-only data: relevance to DNA barcoding

DNA barcoding, as it is currently employed, enhances use of marine benthic macrofauna as environmental condition indicators by improving the speed and accuracy of the underlying taxonomic identifications. The next generation of barcoding applications, processing bulk environmental samples, will likely only provide presence information. However, macrofauna indices presently used to interpret these data are based on species abundances. To assess the importance of this difference, we evaluated the performance of the Southern California Benthic Response Index (BRI) and the AZTI Marine Biotic Index (AMBI) when species abundance data were removed from their calculation. Presence only versions of these two indices were created by eliminating abundance weighting while preserving species identity. Associations between the presence and abundance BRI, and the presence and abundance AMBI were highly significant, with correlation coefficients of 0.99 and 0.81, respectively. The presence versions validated almost equally to the abundance-based indices when applied to the spatial and the temporal monitoring data used to validate the original indices. Simulations in which taxa were systematically removed from calculation of the indices were also conducted to assess how large the barcode library must be for the indices to be effective. Correlation between the BRI-P and BRI remained above 0.9 with only 370 species in the library and reducing the number of species to 450 had almost no effect on correlation between the presence and abundance versions of the AMBI.

Ecological quality assessment of small estuaries from the Portuguese coast based on benthic macroinvertebrate assemblages indices

Benthic macroinvertebrates communities are the most consistently emphasized biotic component of aquatic ecosystems and are one of the biological indicators required for assessment by the European Water Framework Directive. In this context, several indices based on these communities have been developed in order to assess ecological quality of estuarine systems. In the present work we used AMBI, M-AMBI, BENTIX and BAT to distinguish ecological status of five small estuarine systems of the Portuguese south and southwest coasts. Although indices outputs did not differ between systems and sampling seasons, results indicated that the metrics in which these indices are based could differentiate community structures as a result of two main gradients that force these communities: the natural variability, and the anthropogenic impact.

The challenge of choosing environmental indicators of anthropogenic impacts in estuaries

Ecological assessments over large spatial scales require that anthropogenic impacts be distinguishable above natural variation, and that monitoring tools are implemented to maximise impact detection and minimise cost. For three heavily modified and four relatively 'pristine' estuaries (disturbance category), chemical indicators (metals and PAHs) of anthropogenic stress were measured in benthic sediments, suspended sediments and deployed oysters, together with other environmental variables. These were compared with infaunal and hard-substrate invertebrate communities. Univariate analyses were useful for comparing contaminant loads between different monitoring tools and identified the strongest relationships between benthic and suspended sediments. However, multivariate analyses were necessary to distinguish ecological response to anthropogenic stressors from environmental "noise" over a large spatial scale and to identify sites that were being impacted by contaminants. These analyses provide evidence that suspended sediments are a useful alternative monitoring tool to detect potential anthropogenic impacts on benthic (infaunal and hard-substrate) communities.

A novel tolerance range approach for the quantitative assessment of ecosystems

This paper develops a novel tolerance range approach that allows for the quantitative assessment of ecosystems with only a minimum amount of information. The quantitative assessment is achieved through the determination of tolerance range scores and indices that indicate the vulnerability of species. For the purposes of demonstrating the tolerance range approach an ecosystem assessment is performed on Te Waihora/Lake Ellesmere, a large shallow lake found in the Canterbury region of New Zealand. From the analysis of tolerance range scores and indices it was found that brown trout and lake-margin vegetation are the most vulnerable species of value to further degradation. This information implies that management actions should prioritize towards preserving these species to maintain all valued species along sustainable pathways.

Spearfishing regulation benefits artisanal fisheries: the ReGS indicator and its application to a multiple-use Mediterranean marine protected area

The development of fishing efficiency coupled with an increase of fishing effort led to the overexploitation of numerous natural marine resources. In addition to this commercial pressure, the impact of recreational activities on fish assemblages remains barely known. Here we examined the impact of spearfishing limitation on resources in a marine protected area (MPA) and the benefit it provides for the local artisanal fishery through the use of a novel indicator. We analysed trends in the fish assemblage composition using artisanal fisheries data collected in the Bonifacio Strait Natural Reserve (BSNR), a Mediterranean MPA where the spearfishing activity has been forbidden over 15% of its area. Fish species were pooled into three response groups according to their target level by spearfishing. We developed the new flexible ReGS indicator reflecting shifts in species assemblages according to the relative abundance of each response group facing external pressure. The catch per unit effort (CPUE) increased by ca. 60% in the BSNR between 2000 and 2007, while the MPA was established in 1999. The gain of CPUE strongly depended on the considered response group: for the highly targeted group, the CPUE doubled while the CPUE of the untargeted group increased by only 15.5%. The ReGS value significantly increased from 0.31 to 0.45 (on a scale between 0 and 1) in the general perimeter of this MPA while it has reached a threshold of 0.43, considered as a reference point, in the area protected from spearfishing since 1982. Our results demonstrated that limiting recreational fishing by appropriate zoning in multiple-use MPAs represents a real benefit for artisanal fisheries. More generally we showed how our new indicator may reveal a wide range of impacts on coastal ecosystems such as global change or habitat degradation.

Benthic diversity gradients and shifting baselines: implications for assessing environmental status

The increasing pressure on marine biodiversity emphasizes the importance of finding benchmarks against which to assess change. This is, however, a notoriously difficult task in estuarine ecosystems, where environmental gradients are steep, and where benthic biodiversity is highly variable in space and time. Although recent emphasis on diverse, healthy benthic communities in legislative frameworks has increased the number of indices developed for assessing benthic status, there is a lack of quantitative baselines in benthic diversity that would enable comparisons across broad spatial scales, encompassing different environmental settings and bioregions. By taking advantage of long-term monitoring data, spanning hundreds of stations over the past 40 years, we provide a comprehensive analysis of benthic a, beta, and gamma diversity, encompassing the entire' salinity gradient of the open sea areas of the large, brackish-water Baltic Sea. Using a relatively simple measure, average regional diversity, we define area-specific reference conditions and acceptable deviation against which to gauge current conditions in benthic macrofaunal diversity. Results show a severely impaired condition throughout large areas of the Baltic for the assessment period 2001-2006. All ecosystems are plagued by baselines that shift in time and space, and their definition is not trivial, but average regional diversity may offer a transparent way to deal with such changes in low-diversity systems. Identifying baselines will be of increasing importance given the potential of climatic drivers to interact with local anthropogenic stressors to affect patterns of biodiversity. Our analysis provides an evaluation of the current condition in a system that has been heavily influenced by anthropogenic impact and changing oceanographic conditions, and it provides a basis for future impact assessment and ecosystem-based management.