The Benthic Index of Biotic Integrity (B-IBI) was developed and is currently employed for environmental assessment in Chesapeake Bay. The index consists of a variety of benthic community metrics (e.g. abundance, biomass, diversity, stress tolerance groups, etc.) scored by thresholds applied to seven benthic community habitats (tidal freshwater, oligohaline, low mesohaline, high mesohaline mud, high mesohaline sand, polyhaline mud, and polyhaline sand) This index was verified as being a sensitive and robust tool for summarizing the status of benthic communities. In our study we tested the classification efficiency of the index using new benthic data by characterizing each sample a priori as degraded or undegraded using criteria of sediment contaminant levels, bioassays and bottom dissolved oxygen levels. A primary objective of our study was to test the classification efficiency of the B-IBI in small water bodies connected to larger water bodies of the mainstems of the large rivers of Chesapeake Bay, as well as the efficiency of the index over time (1990 through 2009). The B-IBI was affected by the size of the water body, e.g., index accuracy was higher for water bodies in small watersheds in lower salinity habitats, whereas large water bodies of the mainstem of rivers were better classified by the B-IBI in habitats with higher salinities. Across the seven benthic habitat types overall correct classification was moderate to low and lower for correctly classifying undegraded sites. In general the index metrics showed some deficiencies that suggest improvements could be made by recalibrating existing metric thresholds or selecting new suitable metrics.

Human development has degraded Chesapeake Bay's health, resulting in an increase in the extent and severity of hypoxia (≤2 mg O2 l-1). The Bay's hypoxic zones have an adverse effect on both community structure and secondary production of macrobenthos. From 1996 to 2004, the effect of hypoxia on macrobenthic production was assessed in Chesapeake Bay and its three main tributaries (Potomac, Rappahannock, and York Rivers). Each year, in the summer (late July − early September), 25 random samples of the benthic macrofauna were collected from each system, and macrobenthic production in the polyhaline and mesohaline regions was estimated using Edgar's allometric equation. Fluctuations in macrobenthic production were significantly correlated with dissolved oxygen. Macrobenthic production was 90 % lower during hypoxia relative to normoxia. As a result, there was a biomass loss of ~7,320–13,200 metric tons C over an area of 7,720 km2, which is estimated to equate to a 20 % to 35 % displacement of the Bay's macrobenthic productivity during the summer. While higher consumers may benefit from easy access to stressed prey in some areas, the large spatial and temporal extent of seasonal hypoxia limits higher trophic level transfer, via the inhibition of macrobenthic production. Such a massive loss of macrobenthic production would be detrimental to the overall health of the Bay, as it comes at a time when epibenthic and demersal predators have high-energy demands.

The AZTI Marine Biotic Index (AMBI) requires less geographically-specific calibration than other benthic indices, but has not performed as well in US coastal waters as it has in the European waters for which it was originally developed. Here we examine the extent of improvement in index performance when the Ecological Group (EG) classifications on which AMBI is based are derived using local expertise. Twenty-three US benthic experts developed EG scores for each of three regions in the United States, as well as for the US as a whole. Index performance was then compared using: (1) EG scores specific to a region, (2) national EG scores, (3) national EG scores supplemented with standard international EG scores for taxa that the US experts were not able to make assignments, and (4) standard international EG scores. Performance of each scheme was evaluated by diagnosis of condition at pre-defined good/bad sites, concordance with existing local benthic indices, and independence from natural environmental gradients. The AMBI performed best when using the national EG assignments augmented with standard international EG values. The AMBI using this hybrid EG scheme performed well in differentiating apriori good and bad sites (>80% correct classification rate) and AMBI scores were both concordant and correlated (rs=0.4–0.7) with those of existing local indices. Nearly all of the results suggest that assigning the EG values in the framework of local biogeographic conditions produced a better-performing version of AMBI. The improved index performance, however, was tempered with apparent biases in score distribution. The AMBI, regardless of EG scheme, tended to compress ratings away from the extremes and toward the moderate condition and there was a bias with salinity, where high quality sites received increasingly poorer condition scores with decreasing salinity.

Assessing benthic quality status of marine and transitional water habitats requires to set up both: (i) tools (i.e. indices) to assess the relative quality of the considered habitat, and (ii) reference conditions for which such indices can be computed and used to infer the absolute ecological status (ES) of the considered habitat. The development of indices, their comparison and the assessment of the causes of their discrepancies have been largely discussed but less attention has been paid to the methods used for the setting of adequate reference conditions, although this step is clearly crucial for the sound assessment of ES. This contribution reviews the approaches available in setting both reference conditions (pristine areas, hindcasting, modelling and best professional judgment) and targets (baseline set in the past, current baseline and directional/trends). We scored the use of pristine or minimally impacted conditions as the best single method; however, the other methods were judged as adequate then combined with best professional judgment. The case of multivariate AMBI (AZTI's Marine Biotic Index) is used to highlight the importance of setting correct reference conditions. Hence, data from 29 references, including 14 countries from Europe and North America, and both coastal (15 cases) and transitional (17 cases) waters, have been used to study the response of multivariate AMBI to human pressures. Results show that the inability of this index to detect human pressure is in most cases linked with the use of inappropriate methods for setting reference conditions. (C) 2011 Elsevier Ltd. All rights reserved.

Benthic indices to support aquatic environmental condition assessments have been more effectively developed for higher than lower salinity habitats. Here we quantify agreement among benthic experts using best professional judgment to assess community condition of mesohaline and tidal freshwater samples from the San Francisco Estuary and Delta, and compare that to a previous study for San Francisco Estuary polyhaline samples. Benthic species abundance data from 20 sites in each habitat were provided to 7 tidal freshwater, and 8 mesohaline, experts who ranked the samples from best to worst condition and placed the samples into 4 condition categories. The average correlation among expert's condition rankings was only 0.38 and 0.29 in the mesohaline and tidal freshwater habitats, respectively, compared to 0.92 in the previous polyhaline study. Pair-wise agreement among expert condition categories averaged 41% and 39%, compared to 70% in the polyhaline. Based on post-exercise discussions among the experts, the differences in agreement among habitats appears related to the use of different indicator taxa and to disturbance regimes in the lower salinity habitats that select for higher proportions of tolerant taxa, confounding assessments at the current level of understanding of benthic response in these habitats. Regardless of the reason, the absence of a clear conceptual model and agreement among benthic ecologists about benthic condition makes index development more difficult in low salinity estuarine and tidal freshwater habitats. (C) 2011 Elsevier Ltd. All rights reserved.

Many estuarine and coastal marine ecosystems have increasingly experienced degradation caused by multiple stressors. Anthropogenic pressures alter natural ecosystems and the ecosystems are not considered to have recovered unless secondary succession has returned the ecosystem to the pre-existing condition or state. However, depending upon the scales of time, space and intensity of anthropogenic disturbance, return along the historic trajectory of the ecosystem may: (1) follow natural restoration though secondary succession; (2) be re-directed through ecological restoration, or (3) be unattainable. In order to address the gaps in knowledge about restoration and recovery of estuarine and coastal ecosystems, this special feature includes the present overview and other contributions to provide a synthesis of our knowledge about recovery patterns, rates and restoration effectiveness. From the 51 examples collated in this contribution, we refine the recovery from the list of stressors into six recovery mechanisms: (1) recovery from sediment modification, which includes all aspects of dredging and disposal; (2) recovery by complete removal of stressors limiting natural ecosystem processes, which includes tidal marsh and inundation restoration; (3) recovery by speed of organic degradation, which includes oil discharge, fish farm wastes, sewage disposal, and paper mill waste; (4) recovery from persistent pollutants, which includes chemical discharges, such as TBT; (5) recovery from excessive biological removal, related to fisheries and (6) recovery from hydrological and morphological modification. Drawing upon experience both from these many examples and from an example of one comprehensive study, we show that although in some cases recovery can take <5 years, especially for the short-lived and high-turnover biological components, full recovery of coastal marine and estuarine ecosystems from over a century of degradation can take a minimum of 15–25 years for attainment of the original biotic composition and diversity may lag far beyond that period.

Abstract Spionid polychaetes are a dominant component of benthic assemblages in marine and estuarine habitats and are important in assessing ecological function and integrity. Ecological and biogeographic studies rely upon the ability to distinguish between morphologically similar species, as well as knowledge of evolutionary relationships between species. Unfortunately, differentiating between congeneric species of spionids can be challenging thereby potentially creating mistakes in scientific investigations. For example Streblospio contains three recognized species (S. benedicti, S. shrubsolii, S. gynobranchiata) with few distinguishing morphological characters. Herein, we use ∼500 bases of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) to investigate the status of S. shrubsolii relative to other Streblospio. COI has previously been used to distinguish North American Streblospio benedicti and S. gynobranchiata. Results indicate all three Streblospio species are reciprocally monophyletic with S. shrubsolii basal to a well-supported S. benedicti/S. gynobranchiata clade.

To meet the requirements of the Clean Water Act, the States of Maryland and Virginia are using benthic biological criteria for identifying impaired waters in Chesapeake Bay and reporting their overall condition. The Chesapeake Bay benthic index of biotic integrity (B-IBI) is the basis for these biological criteria. Working together with the states and the US Environmental Protection Agency, we developed a method for impairment decisions based on the B-IBI. The impaired waters decision approach combines multiple benthic habitat-dependent indices in a Bay segment (equivalent to water bodies in the European Water Framework Directive) with a statistical test of impairment. The method takes into consideration uncertainty in reference conditions, sampling variability, multiple habitats, and sample size. We applied this method to 1430 probability-based benthic samples in 85 Chesapeake Bay segments. Twenty-two segments were considered impaired for benthic community condition. The final decision for each segment considers benthic condition in combination with key stressors such as dissolved oxygen and toxic contaminants.

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

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

Mangroves are multi-functional ecosystems providing resource provisions and various ecosystem services, all of which are critical to the local livelihood and national economy. However, unsustainable anthropogenic activities continue to undermine the health of these ecosystems resulting in environmental adversities and declining resources. This study aimed to formulate a Mangrove Quality Index (MQI) which took into consideration the mangrove forest, contributing components of a mangrove forest, soil, surrounding marine ecosystem, hydrology and the socio-economic variables. Three major sites representing the least, moderately and most-disturbed mangrove ecosystems in Matang, Malaysia were selected. These areas were used to assess the contribution of 43 variables from five categories, namely, mangrove biotic integrity, mangrove soil, marine-mangrove, mangrove hydrology, and mangrove socio-economic factors. Two types of indices were developed to indicate the status of each category, 1) Mangrove Quality Index for a specific category (MQISi) and, 2) Overall MQI to reflect the overall health status of the ecosystem. The indices for the five different categories were Mangrove Biotic Integrity Index (MQIS1), Mangrove Soil Index (MQIS2), Marine-Mangrove Index (MQIS3), Mangrove-Hydrology Index (MQIS4) and Mangrove-Socio-economic Index (MQIS5). Using Principle Component Analysis, ten variables representing all the five categories were selected to formulate the overall MQI. They are aboveground biomass, crab abundance, soil carbon, soil nitrogen, number of phytoplankton species, number of diatom species, dissolved oxygen, turbidity, education level, and time spent fishing. We developed the overall MQI based on the total score obtained from each category. The health status of mangroves is ranked from 1 to 5 viz. 1 (worst), 2 (bad), 3 (moderate), 4 (good), 5 (excellent). In the Matang Mangrove, the health status of the least disturbed area is ranked 5, moderate disturbed area is ranked 4, while the most disturbed area is ranked 2. The Normalized Difference Vegetation Index (NDVI) supported the overall MQI developed. The NDVI for the least disturbed area in Matang ranged from −0.689846 to 0.652204, for the moderately disturbed area, it ranged from −0.732508 to 0.638625, while the most disturbed area ranged from −0.916667 to 0.314991.

Benthic communities provide secondary production for higher trophic levels, and changes in benthic community structure can be a harbinger for associated food web alterations. Benthic communities can be affected by variations in water quality, with low dissolved oxygen reducing benthic abundance and biomass. We quantified the effects of dissolved oxygen and other environmental factors upon changes in density, biomass, and diversity of the macrobenthic community from long-term data (1996–2004) from the Chesapeake Bay Program's benthic monitoring. Benthic density, biomass, and diversity were significantly and negatively correlated with water depth and positively correlated with the dissolved oxygen level. In an assessment of multiple models using Akaike's Information Criteria, oxygen was the single best predictor of summer benthic infaunal density by depth. Biomass was best predicted by depth, salinity, and dissolved oxygen together. Moreover, oxygen was among the important factors determining Shannon (H′) diversity. Benthic diversity in Chesapeake Bay over 2001–2004 was historically low compared to that over the years 1996–2000 and was directly correlated with the severity of hypoxia. Hypoxia leads to mass mortality of benthos, which reduces the overall availability of secondary production to higher trophic levels and can affect overall productivity in Chesapeake Bay. Regions with low dissolved oxygen should be managed to minimize deleterious anthropogenic effects on benthos that may affect higher trophic levels.

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

Benthic infaunal communities are frequently used to assess aquatic environmental condition, but interpretation of benthic data is often subjective and based on best professional judgment. Here, we examine the repeatability of such assessments by providing species-abundance data from 35 sites to 9 independent benthic experts who ranked the sites from best to worst condition. Their site rankings were highly correlated, with an average correlation coefficient of 0.91. The experts also evaluated the sites in terms of four condition categories: (1) unaffected, (2) marginal deviation from reference, (3) affected, or (4) severely affected. At least two-thirds of the experts agreed on site categorization for 94% of the samples and they disagreed by more than one category for less than 1% of the assessment pairs. The experts identified seven parameters used in making their assessments, with four of those parameters (dominance by tolerant taxa, presence of sensitive taxa, species richness, and total abundance) used by all of the experts. Most of the disagreements in site categorization were due to philosophical rather than technical differences, such as whether the presence of invasive species indicates a degraded community. Indices are increasingly being used as an alternative to best professional judgment for assessing benthic condition, but there have been inconsistencies in how sites are selected for validating such indices; the level of agreement found among experts in this study suggests that consensus expert opinion can be a viable benchmark for such evaluations.

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

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

We tested whether macrobenthic community condition varies significantly with water depth in a variety of regions of Chesapeake Bay, USA. Benthic community condition was characterized using the Benthic Index of Biotic Integrity (B-IBI) previously developed for the Bay. We applied two water depth thresholds intended to emphasize the ecological importance and/or anthropogenic impacts upon shallow-water regions. The first threshold of 2m emphasizes restoring and supporting submerged aquatic vegetation while the second threshold of 4m emphasizes the zone of maximum anthropogenic impact upon natural ecosystem functions. An a priori expectation is that benthic community condition may worsen with increasing depth, specifically in regions (1) where water column stratification at depth results in prolonged low dissolved oxygen levels or (2) where net deposition at depth results in higher levels of hydrophobic, sediment-bound contaminants. Samples collected from a major tributary of Chesapeake Bay, the York River estuary, spanned the entire salinity range from tidal freshwater to polyhaline. We also tested the shallow-water depth thresholds using data from the Virginia Mainstem of Chesapeake Bay and the Southern Branch of the Elizabeth River. These two polyhaline regions are characterized as having the best and worst benthic community condition in Chesapeake Bay. At the scale of the entire tidal York River system, there were no significant differences in benthic community condition with water depth. However, two salinity regions, low mesohaline and polyhaline, had significant depth effects with the shallowest water depth zone significantly different from the other two depth regions. For the low mesohaline region benthic community condition was worse at the shallowest depth and for the polyhaline region the shallowest depth was better comparing the three depth regions. No depth-related differences in the B-IBI were found for the two additional Chesapeake Bay strata, the Virginia Mainstem characterized with the lowest levels of benthic community degradation and for the Southern branch of the Elizabeth River, characterized by the highest levels of benthic community degradation. We conclude that the ecological state of Chesapeake Bay subtidal benthic communities is adequately characterized by randomly sampling all depths without further stratification into shallow and deeper regions.

Increasingly on a worldwide scale, legislation has been adopted to determine the ecological integrity of surface waters including streams, rivers, lakes, estuaries and coastal waters. An integral part of determining ecological integrity is the measurement of biological integrity, typically emphasizing analyses of plankton, benthos, macroalgae and fish. In the development of protocols for evaluating biological integrity, benthic macroinvertebrate communities are the most consistently emphasized biotic component of aquatic ecosystems. A plethora of methodologies with hundreds of indices, metrics and evaluation tools are presently available. An ecologically parsimonious approach dictates that investigators should place greater emphasis on evaluating the suitability of indices that already exist prior to developing new ones. Hence, the authors organized within the American Society of Limnology and Oceanography 2006 Summer Meeting, 4–9 June 2006, in Victoria, BC, Canada, a special session with the objective to compare methodologies, applications and interpretations existing in various countries and attempting to contribute to an improved understanding of the suitability of such approaches when using benthic communities. From the 25 contributions presented in this session, eight manuscripts were selected to be included in this special issue of Ecological Indicators including new index development, novel validation approaches, assessment of spatio-temporal applications, interpretations relative to management needs and potential adaptive management modifications to maximize the robustness, sensitivity, and representativeness of environmental information conveyed to management.

Triad studies consisting of chemical characterizations in sediment, sediment toxicity testing, and benthic community assessments were used to determine the impacts of Motiva Enterprises oil refinery effluent [primarily polynuclear aromatic hydorcarbons (PAHs)] on aquatic biota in the Delaware River. Triad studies were conducted at 15 near-field, mid-field, and far-field sites near the Refinery in the Delaware River during the spring and summer of 2001 and 2002. Fingerprinting analysis showed that Motiva-related PAHs may be present at four near-field sites. A summary of all Triad data by site for 2001 shows a strong case for contaminant-induced degradation at one near-field site in the discharge canal of the Refinery and two far-field sites as all three lines of evidence suggest impairment. Stressful conditions for benthic communities at the near-field site include elevated temperature conditions and various pesticides (Dieldrin, 4,4'-DDD and 4,4'-DDT). Toxicity at the near-field site may also be related to the presence of pesticides exceeding sediment quality guidelines. Due to exceedances of individual Effects Range Low (ERL) guidelines for two individual PAHs, the Motiva effluent cannot be eliminated as a potential stressor at the near-field site during the summer of 2001. A summary of Triad data for the 15 Delaware River sites sampled in 2002 shows only one mid-field site where all three lines of evidence suggest impairment. Toxicity and benthic community impairment at this mid-field site may be related to PCBs and low molecular weight PAHs. Three individual PAH ERL values were exceeded at three near-field sites in 2002. The source of these PAHs is a combination of both background signature and the Motiva effluent. Multivariate analysis, using a weight of evidence approach, is used to address ecological effects of the Motiva effluent in more detail in Alden et al. (2005).