Recent and past studies have documented the prevalence of pyrethroid and organophosphate pesticides in urban and agricultural watersheds in California. While toxic concentrations of these pesticides have been found in freshwater systems, there has been little research into their impacts in marine receiving waters. Our study investigated pesticide impacts in the Santa Maria River estuary, which provides critical habitat to numerous aquatic, terrestrial, and avian species on the central California coast. Runoff from irrigated agriculture constitutes a significant portion of Santa Maria River flow during most of the year, and a number of studies have documented pesticide occurrence and biological impacts in this watershed. Our study extended into the Santa Maria watershed coastal zone and measured pesticide concentrations throughout the estuary, including the water column and sediments. Biological effects were measured at the organism and community levels. Results of this study suggest the Santa Maria River estuary is impacted by current-use pesticides. The majority of water samples were highly toxic to invertebrates (Ceriodaphnia dubia and Hyalella azteca), and chemistry evidence suggests toxicity was associated with the organophosphate pesticide chlorpyrifos, pyrethroid pesticides, or mixtures of both classes of pesticides. A high percentage of sediment samples were also toxic in this estuary, and sediment toxicity occurred when mixtures of chlorpyrifos and pyrethroid pesticides exceeded established toxicity thresholds. Based on a Relative Benthic Index, Santa Maria estuary stations where benthic macroinvertebrate communities were assessed were degraded. Impacts in the Santa Maria River estuary were likely due to the proximity of this system to Orcutt Creek, the tributary which accounts for most of the flow to the lower Santa Maria River. Water and sediment samples from Orcutt Creek were highly toxic to invertebrates due to mixtures of the same pesticides measured in the estuary. This study suggests that the same pyrethroid and organophosphate pesticides that have been shown to cause water and sediment toxicity in urban and agriculture water bodies throughout California, have the potential to affect estuarine habitats. The results establish baseline data in the Santa Maria River estuary to allow evaluation of ecosystem improvement as management initiatives to reduce pesticide runoff are implemented in this watershed.

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.

The spatial and temporal distribution of macrobenthic assemblages in the San Francisco Estuary and Sacramento–San Joaquin River Delta were identified using hierarchical cluster analysis of 501 samples collected between 1994 and 2008. Five benthic assemblages were identified that were distributed primarily along the salinity gradient: (1) a polyhaline assemblage that inhabits the Central Bay, (2) a mesohaline assemblage that inhabits South Bay and San Pablo Bay, (3) a low-diversity oligohaline assemblage primarily in Suisun Bay, (4) a low-diversity sand assemblage that occurs at various locations throughout the Estuary, and (5) a tidal freshwater assemblage in the Delta. Most sites were classified within the same assemblage in different seasons and years, but a few sites switched assemblage designations in response to seasonal changes in salinity from freshwater inflows.

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.

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.

AbstrAct Benthic indices used to assess sediment quality are based on having abundance data for all species in the community. Molecular genetic approaches, including DNA barcoding provide promise for improving the speed and accuracy of taxonomic identifications. Future application of DNA barcoding by analyzing bulk environmental samples through next-generation sequencing will enable rapid species identification, but this gain may be offset by the inability of these methods to quantify species abundances. To address this issue we evaluated the performance of the Southern California Benthic Response Index (BRI) when species abundance data were removed from its calculation. The presence BRI was created by eliminating abundance weighting while preserving species identity. The relationship between the presence and abundance BRI was highly significant, with an r2 = 0.98. The presence BRI also validated almost equally to the abundance BRI when applied to the spatial and the temporal monitoring data used to validate the original BRI. Simulations were conducted to assess how large the barcode library must be for an effective index, with changes in the r2 between the presence and abundance BRI determined as taxa were systematically removed from calculation of the presence BRI. The r2 remained above 0.8 with fewer than 400 species in the library.

Data from 7 coastwide and regional benthic surveys were combined and used to assess the number and distribution of estuarine benthic macrofaunal assemblages of the western United States. Q‐mode cluster analysis was applied to 714 samples and site groupings were tested for differences in 4 habitat factors (latitude, salinity, sediment grain size, and depth). Eight macrofaunal assemblages, structured primarily by latitude, salinity, and sediment grain size, were identified: (A) Puget Sound fine sediment, (B) Puget Sound coarse sediment, (C) southern California marine bays, (D) polyhaline central San Francisco Bay, (E) shallow estuaries and wetlands, (F) saline very coarse sediment, (G) mesohaline San Francisco Bay, and (H) limnetic and oligohaline. The Puget Sound, southern California, and San Francisco Bay assemblages were geographically distinct, while Assemblages E, F and H were distributed widely along the entire coast. A second Q‐mode cluster analysis was conducted after adding replicate samples that were available from some of the sites and temporal replicates that were available for sites that were sampled in successive years. Variabilities due to small spatial scale habitat heterogeneity and temporal change were both low in Puget Sound, but temporal variability was high in the San Francisco estuary where large fluctuations in freshwater inputs and salinity among years leads to spatial relocation of the assemblages. Integr Environ Assess Manag 2012; 8: 638–648. © 2010 SETAC

Benthic indices are useful indicators of sediment condition, but many indices are difficult to employ because they require large calibration datasets. The AZTI's Marine Biotic Index (AMBI) requires minimal local calibration, but it was developed in Europe and the validity of its extension to distant regions is unclear. Here we compare its performance in Southern California's marine bays with that of the Benthic Response Index (BRI), a locally derived data-intensive index. AMBI was calibrated in four ways: (1) using the original AMBI species' classifications developed in Europe; (2) augmenting the original classifications with closely related taxa, following AMBI guidelines; (3) using local expertise to independently classify taxa; and (4) revision of the local expert classifications by European developers of the index. These approaches were applied to a 685 sample data set and assessed relative to the BRI by comparing samples' classification from best to worst and by evaluating the level of agreement in assigning samples into four condition categories. The AMBI was validated against environmental proxies of disturbance and expert judgement, using consensus agreement about sample condition developed by nine benthic ecologists. The first AMBI approach did not work well, as only 24% of the 928 taxa were on the original AMBI species list, resulting in only 11% of the samples meeting the required 20% of classified individuals for AMBI application. The other approaches classified substantially more taxa, allowing application to 75-98% of the samples. Both of these approaches were significantly correlated with the BRI, though the correlations were lower than between the AMBI runs. None of the AMBI approaches, though, compared well with either the BRI or the validation data when placing samples into perturbation categories, with the AMBI having a greater central tendency. AMBI categorized less than 5% of the samples as reference compared to almost one-third of the samples by the experts or BRI, and substantially underestimating the number of severely affected samples. Species most responsible for disagreements between BRI and AMBI approaches were identified. Four modifications to enhance AMBI performance were identified: (1) incorporate local expertise in assigning ecological classifications, (2) use transformed abundance weighting to reduce the effect of dominant species, (3) calibrate the categorization scaling using expert judgement, and (4) use the AMBI in combination with other measures, such as the M-AMBI. The success of these modifications is specific to this study, but they are likely to enhance AMBI's performance worldwide. (C) 2011 Elsevier Ltd. All rights reserved.

To assess benthic macrofaunal community condition in Southern California, 838 sites were sampled using spatially random designs in 1994, 1998, or 2003. Benthic community condition was assessed on a four-category scale and the area in each category estimated. Overall, benthic macrofauna in Southern California were in good condition during 2003, with 98% of the area in reference condition or deviating only marginally. There was no evidence of disturbance near Channel Islands or small wastewater discharges, and virtually none on the mainland shelf. In contrast, bay and estuary macrofaunal communities were more frequently disturbed with nearly 13% of the area supporting disturbed benthos. The condition of the mainland shelf did not change substantially over the 9-year period, with 1.6–2.8% of the area in poor benthic condition. Southern California benthic condition evaluations may be improved by extending the depth and salinity ranges of assessment tools, and improving trend detection methods.

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.

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.

Many types of indices have been developed to assess benthic invertebrate community condition, but there have been few studies evaluating the relative performance of different index approaches. Here we calibrate and compare the performance of five indices: the Benthic Response Index (BRI), Benthic Quality Index (BQI), Relative Benthic Index (RBI), River Invertebrate Prediction and Classification System (RIVPACS), and the Index of Biotic Integrity (IBI). We also examine whether index performance improves when the different indices, which rely on measurement of different properties, are used in combination. The five indices were calibrated for two geographies using 238 samples from southern California marine bays and 125 samples from polyhaline San Francisco Bay. Index performance was evaluated by comparing index assessments of 35 sites to the best professional judgment of nine benthic experts. None of the individual indices performed as well as the average expert in ranking sample condition or evaluating whether benthic assemblages exhibited evidence of disturbance. However, several index combinations outperformed the average expert. When results from both habitats were combined, two four-index combinations and a three-index combination performed best. However, performance differences among several combinations were small enough that factors such as logistics can also become a consideration in index selection.

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.

During the last decade, there have been substantial scientific advances in the development of indices that measure the condition of biological ecosystem elements in coastal and estuarine waters. Though successful, these advances were only the initial steps and a special session on use of indices in ecological integrity assessments was held at the Coastal and Estuarine Research Federation meeting to focus the field on the most appropriate directions for the next decade. The session identified four primary scientific challenges: (i) reduce the array of indices by identifying the index approaches that are most widely successful; (ii) establish minimum criteria for index validation; (iii) intercalibrate methods to achieve uniform assessment scales across geographies and habitats; and (iv) integrate indices across ecosystem elements. Where an explosion of indices characterized the last decade, the next decade needs to be characterized by consolidation. With increased knowledge and understanding about the strengths and weaknesses of competing index approaches, the field needs to unify approaches that provide managers with the simple answers they need to use ecological condition information effectively and efficiently.

The prevalence of non-indigenous species (NIS) in southern California embayments was assessed from 123 Van Veen grab samples collected in nine bays and harbors during the summer of 1998. NIS occurred in all but two samples. They accounted for only 4.3% of the 633 taxa but contributed 27.5% of the abundance. There was no significant difference in the proportion of NIS abundance among ports harboring large vessels, small boat marinas, and areas where boats were not moored. Three species accounted for 92% of the NIS abundance: a spionid polychaete worm Pseudopolydora paucibranchiata, a mytilid bivalve Musculista senhousia, and a semelid bivalve Theora ubrica. The NIS did not appear to have a negative impact at the overall community level since NIS abundance was positively correlated with the abundance and richness of other species. This may be due to biogenic structures built by P. paucibranchiata and M. senhousia that enhance the abundances of other macrofauna.

The prevalence of nonindigenous species (NIS) and their effects on benthic macroinvertebrate communities in southern California embayments was assessed by collecting 113 Van Veen Grab samples from nine bays and harbors during the summer and fall of 1998. NIS accounted for only 4% of the 617 taxa encountered but contributed 28% of abundance. NIS abundance was evenly distributed with no systematic differences among ports servicing large ocean-going vessels or small boat marinas. NIS in non-boat mooring areas were about half as frequent. Three species were responsible for 92% of the NIS abundance: a spionid polychaete worm Pseudopolydora paucibranchiata, a mytilid bivalve Musculista senhousia, and a semelid bivalve Theora lubrica. NIS did not appear to have a negative impact of the communities since NIS abundance was positively correlated with both abundance and richness of native species. P. paucibranchiata and M. senhousia create additional physical habitat structures that facilitate the presence of native infauna.