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

Impacts of habitat alteration on macroinvertebrates in large shallow lakes: An application of a macroinvertebrate-based multimetric index

Habitat plays a crucial role in shaping the macroinvertebrate community structure in large shallow lakes. In the pursuit of improving the health of freshwater ecosystems, it is imperative to consider their habitat characteristics. To evaluate the impact of habitat variations on lake ecological health, we developed a macroinvertebrate-based multimetric index (MMI) for both the pelagic and littoral zones of Lake Hongze. Additionally, we employed structural equation models to explore the influence of utilization or phytoplankton biomass on ecological health. Historical data served as reference conditions for the pelagic. Seven key attributes were selected for the pelagic MMI, that is, Biological Monitoring Working Party (BMWP), the percentage of Mollusca taxa, the percentage of filter-collector taxa, the percentage of predator taxa, the percentage of gather-collector taxa, and the percentage of sensitive taxa and functional dispersion. The least minimally disturbed conditions and the best attainable conditions were used to develop the littoral. Four key metrics, that is, the percentage of scraper abundance, Mollusca taxa, Biological Pollution Index, and BMWP, were integrated into the littoral MMI. The assessment based on MMI revealed a "poor" health status for the pelagic zone and a "fair" health status for the littoral zone. These findings underscore the high applicability and efficacy of MMIs in assessing and monitoring ecological health in Lake Hongze. Notably, functional feeding groups exhibited heightened sensitivity to disturbance in both zones. Moreover, sediment organic matter strongly influenced the pelagic ecological health, while chlorophyll a and transparency emerged as primary factors influencing the littoral zone, attributable to varying littoral zone utilization. Integr Environ Assess Manag 2024;00:1-11. © 2024 SETAC.

Assessing river water quality for ecological risk in the context of a decaying river in India

The decay of rivers and river water pollution are common problems worldwide. However, many works have been performed on decaying rivers in India, and the status of the water quality is still unknown in Jalangi River. To this end, the present study intends to examine the water quality of the Jalangi River to assess ecological status in both the spatial and seasonal dimensions. To depict the spatiality of ecological risks, 34 water samples were collected from the source to the sink of the Jalangi River with an interval of 10 km while 119 water samples were collected from a secondary source during 2012-2022 to capture the seasonal dynamics. In this work, the seasonality and spatiality of change in the river's water quality have been explored. This study used the eutrophication index (EI), organic pollution index (OPI), and overall index of pollution (OIP) to assess the ecological risk. The results illustrated that the values of OPI range from 7.17 to 588, and the values of EI exceed the standard of 1, indicating the critical situation of the ecological status of Jalangi River. The value of OIP ranges between 2.67 and 3.91 revealing the slightly polluted condition of the river water. The study signified the ecological status of the river is in a critical situation due to elevated concentrations of biological oxygen demand, chemical oxygen demand, and low concentrations of dissolved oxygen. The present study found that stagnation of water flow in the river, primarily driven by the eastward tilting of the Bengal basin, triggered water pollution and ecological risk. Moreover, anthropogenic interventions in the form of riverbed agriculture and the discharge of untreated sewage from urban areas are playing a crucial role in deteriorating the water quality of the river. This decay needs substantial attention from the various stakeholders in a participatory manner.

Submarine outfall and new sewage treatment plant modulate the response of intertidal benthic communities in a SW Atlantic area

Spatio-temporal responses of the intertidal macrobenthic community to the effects of a submarine outfall (SO) and a new sewage treatment plant (EDAR) were evaluated, analyzing changes in macrofaunal assemblages and community structure. Study was conducted in a SW Atlantic coastal area in 4 stages: BSO (Before the SO), Du (During the construction of the SO), ASO (After the SO start-up) and AEDAR (After the treatment plant start-up). Boccardia proboscidea and Brachidontes rodriguezii contributed most to the differences between all stages at the site nearest to the discharge point. Number of individuals was highest at BSO and Du. Richness and diversity were lowest at the BSO and highest at the Du. Furthermore, the richness decreased slightly, and the diversity increased at AEDAR. Evenness was highest at the BSO and AEDAR. The nestedness was the dominant process driving the differences between the BSO stage community and the rest of the stages. SO affects the composition and structure of the intertidal macrobenthic community near the outfall area, as organic matter discharge further offshore favour the development of a more diverse intertidal community, including species sensitive to organic enrichment.

Unlocking foraminiferal genetic diversity on estuarine mudflats with eDNA metabarcoding

Environmental biomonitoring is a prerequisite for efficient evaluation and remediation of ecosystem degradation due to anthropogenic pressure or climate change. Estuaries are key habitats subject to multiple anthropogenic and natural stressors. Due to these multiple stressors, the detection of anthropogenic pressure is challenging. The fact that abundant natural stressors often lead to negative quality assessments has been coined the "estuarine quality paradox". To solve this issue, the application of molecular approaches with successful bioindicators like foraminifera is promising. However, sampling protocols, molecular procedures and data analyses need to be validated before such tools can be routinely applied. We conducted an environmental DNA survey of estuarine mudflats along the French Atlantic coast, using a metabarcoding approach targeting foraminifera. Our results demonstrate that estuarine environments have only a few active OTUs dominating the community composition and a large stock of dormant or propagule stages. This last genetic diversity components constitute an important reservoir, with different species which can potentially develop in response to the temporal variability of the multiple stressors. In fact, different OTUs were dominant in the studied estuaries. Our statistical model shows that the physical and chemical characteristics of the sediment and the climatic conditions explain only 43 % of the community composition variance. This suggests that other, less easily quantifiable factors, such as the history and use of the estuaries or the ecological drift could play an important role as well. Environmental DNA biomonitoring opens new perspectives to better characterize the genetic diversity in estuaries.

Evaluating the effectiveness of M-AMBI with other biotic indexes in a temperate estuary

Need for a scalable and widely applicable index has been increasingly important. This study evaluates the applicability of the M-AMBI, a potential comprehensive index, at small spatial scales. M-AMBI was compared to regional indices (EMAP-E and GOM B-IBI), assessing response to natural environmental gradients and low oxygen stress. Results indicate poor agreement between indices with M-AMBI and GOM B-IBI showing positive correlation but significant disagreement in habitat condition. EMAP-E had no agreement. Indices showed similar patterns of better habitat scores in higher salinities. M-AMBI also showed a negative relationship with sediment organic matter and total nitrogen. DO influenced all indices with M-AMBI the most sensitive. However, mismatches between DO and index score were observed further calibration may be needed before adoption into programs. Overall, the M-AMBI demonstrates potential at smaller, local scales, but additional studies are needed to validate its performance in different coastal environments and under different conditions.

eDNA metabarcoding reveals shifts in sediment eukaryote communities in a metal contaminated estuary

Metal contamination is a global issue impacting biodiversity in urbanised estuaries. Traditional methods to assess biodiversity are time consuming, costly and often exclude small or cryptic organisms due to difficulties with morphological identification. Metabarcoding approaches have been increasingly recognised for their utility in monitoring, however studies have focused on freshwater and marine systems despite the ecological significance of estuaries. We targeted estuarine eukaryote communities within the sediments of Australia's largest urbanised estuary, where a history of industrial activity has resulted in a metal contamination gradient. We identified specific eukaryote families with significant correlations with bioavailable metal concentrations, indicating sensitivity or tolerance to specific metals. While polychaete families Terebellidae and Syllidae demonstrated tolerance to the contamination gradient, members of the meio- and microfaunal communities including diatoms, dinoflagellates and nematodes displayed sensitivities. These may have high value as indicators but are frequently missed in traditional surveys due to sampling limitations.

Assessing the ecological quality status of macrobenthic communities in a marine terminal of liquefied natural gas in Peru

Macrobenthic organisms are useful bioindicators to assess ecological quality status. On the south-central coast of Peru (13°15.15'S, 76°18.5'W), a Liquefied Natural Gas (LNG) marine terminal has been operating since 2010. We investigated the macrobenthic communities and sediment parameters from 2011 to 2020 to evaluate the ecological quality status in the surrounding area of the marine terminal, using the AZTI Marine Biotic Index (AMBI) and its multivariate version (M-AMBI). We analyzed the diversity and community composition of macrobenthic invertebrates and the physico-chemical parameters of the sediment from 29 sampling sites, ranging from 0 to 15m depth. The sampling design considered: the direct influence zone ("DIZ", surroundings of the marine terminal), and northern (NCZ) and southern (SCZ) control zones. Our results indicated that abundance was high at SCZ and decreased with depth. Species richness and diversity were high at DIZ and NCZ, respectively, and increased up to 10m but dropped at 15m. High sand content was recorded in shallow depths, while in deeper areas and DIZ, mud and organic matter increased and redox potential was negative. AMBI indicated a "slightly disturbed" status in general, while M-AMBI indicated "good" or "moderate" status at depths ≤ 12m, and "poor" status at 15m. Overall, the season/year factor was not important, and variables were mostly significantly different across depths. Redox potential and organic matter were correlated with M-AMBI at 15m. In general, our results indicate an acceptable ecological quality surrounding the marine terminal, likely because the study area is not influenced by an important input of an anthropogenic stressor. This study highlights the importance of monitoring benthic communities in the surroundings of human-made structures and the use of ecological quality indices for understanding potential impacts.

Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding

Aquaculture impacts on marine benthic ecosystems are widely recognized and monitored. However, little is known about the community changes occurring in the water masses surrounding aquaculture sites. In the present study, we studied the eukaryotic communities inside and outside salmonid aquaculture cages through time to assess the community changes in the neighbouring waters of the farm. Water samples were taken biweekly over five months during the production phase from inside the cages and from nearby points located North and South of the salmon farm. Eukaryotic communities were analyzed by eDNA metabarcoding of the partial COI Leray-XT fragment. The results showed that eukaryotic communities inside the cages were significantly different from those in the outside environment, with communities inside the cages having higher diversity values and more indicator species associated with them. This is likely explained by the appearance of fouling species that colonize the artificial structures, but also by other species that are attracted to the cages by other means. Moreover, these effects were highly localized inside the cages, as the communities identified outside the cages, both North and South, had very similar eukaryotic composition at each point in time. Overall, the eukaryotic communities, both inside and outside the cages, showed similar temporal fluctuations through the summer months, with diversity peaks occurring at the end of July, beginning of September, and in the beginning of November, with the latter showing the highest Shannon diversity and richness values. Hence, our study suggests that seasonality, together with salmonid aquaculture, are the main drivers of eukaryotic community structure in surface waters surrounding the farm.

Species and functional diversity of marine macrobenthic community and benthic habitat quality assessment in semi-enclosed waters upon recovering from eutrophication, Bohai Bay, China

This study investigated the structure and function of macrobenthic community in Bohai Bay upon improvement of water quality due to pollution abatement. A total of 166 species were collected in the summer and autumn sampling, with an increase in sensitive species recorded as compared to data from previous studies. While historical variations in species richness indicated signs of improvement in community structure, results of functional diversity indices revealed that the macrobenthic community in Bohai Bay was still in an early stage of recovery. From BIO-ENV analysis, habitat instability may hinder how community responded to water quality improvement. Results of the benthic habitat quality assessment also indicated that the ecological status in most areas of Bohai Bay was classified as good, while a few estuarine regions were categorized in a poor status.

Assessing ecological health in areas with limited data by using biological traits

A multitude of biotic indices that represent environmental status have been developed over the past decades making status comparisons difficult. However, transferring an existing index to a new region can be problematic due to differing stressors, ecosystem components and lack of knowledge on regional species sensitivities. Here we assess whether calculating species sensitivities to specific stressors based on biological traits offers a solution. We use biological traits of macrofaunal species to assess sensitivity to suspended sediment concentrations and calculated the Benthic Quality Index (BQI) at 47 sites across a suspended sediment gradient. This trait-based modification of the BQI was well correlated (0.82) to suspended sediment. Problems previously highlighted, relating to trait plasticity and differential weightings of indifferent and beneficial species, were investigated but did not strongly affect results. A trait-based approach has the additional benefit that the data could be easily converted to evaluate ecosystem function.

Sex, size and habitat complexity effects on emergence latency and latency to locate food of the invasive porthole livebearer (Poeciliopsis gracilis)

Biological invasions are considered the second major cause of plant, amphibian, reptile, and mammal loss worldwide. Like islands, freshwater ecosystems are especially susceptible to the negative impacts of invasions. The porthole livebearer (Poeciliopsis gracilis), recently identified as invasive in the Mexican Central Plateau, is increasing its populations and could impact freshwater ecosystems like its cousin species the guppy (Poecilia reticulata). Risk-taking behaviours, such as emergence latency, are recognised as key characteristics to invasion success and Poeciliid females can establish a viable population by themselves (due to their multiple paternity broods). We investigated the emergence latency and latency to locate food in simple and complex environments of porthole livebearers, including the effect of their size and sex. For both sexes, bigger fish emerge less times and take longer to do so, but females are faster to exit the refuge than males. We found no differences in porthole livebearer’s behaviour in complex or simple habitats, and no significant differences between sex, size or treatment in the time to locate food after exiting the refuge. Our results suggest that the benefit of faster emergence from the refuge in porthole livebearers in novel environments could be higher for females. We consider that porthole livebearer females being bolder could contribute to the invasion success of the species. Our study points at females and smaller fish as being the more likely to explore novel environments, which could contribute to understanding how the invasions by the porthole livebearer are driven.

Environmental Status and Geomorphological Characterisation of Seven Black Coral Forests on the Sardinian Continental Shelf (NW Mediterranean Sea)

Simple Summary

Black coral forests are three-dimensional components of the marine mesophotic benthic community that play a crucial role in the benthic–pelagic processes, enhancing substrate complexity and creating numerous ecological niches and biodiversity hotspots. The increase of natural and human pressures on these forests is decimating their sophisticated architecture, leading to habitat degradation and biodiversity loss. This study assessed the environmental status of seven black coral forests dwelling in the centre of the Mediterranean Sea using the Mesophotic Assemblages Conservation Status Index. Our results showed how site-specific ecological conditions associated with different geomorphological settings can determine the variability of the environmental status among these habitats. Overall, most of the black coral forests investigated showed a “high” and “good” status; however, in two sites, a degraded benthic community and a marked anthropogenic impact determined a “moderate” and “poor” environmental status, highlighting the fragility of these communities to anthropogenic stressors, even in an area of low urbanisation, such as a Sardinian island. The scenario obtained by this study, combined with a more complete understanding of the processes that drive benthic communities’ dynamics, would facilitate the evaluation of potential measures for the appropriate management of human activities and the general conservation of mesophotic coral forests.

Abstract

Marine animal forests are key mesophotic ecosystems that are under threat from increasing natural and human pressures. Despite the fact that various international agreements strive to preserve these fragile ecosystems, the environmental status of the majority of these animal-structured environments is unknown. Assessing their environmental status is the first step needed to monitor these essential habitats’ health over time and include them within conservation and protection frameworks, such as the Marine Strategy Framework Directive. Based on Multibeam data and ROV footage, we characterized the geomorphological setting and evaluated the environmental status of seven black coral forests in the centre of the Western Mediterranean Sea, using the Mesophotic Assemblages Conservation Status (MACS) Index. The presence of two antipatharians, Antipathella subpinnata and Leiopathes glaberrima, characterized the seven investigated sites, dwelling on rocky substrate characterized by different environmental drivers (i.e., depth, slope of the substrate, terrain ruggedness, topographic positioning index, and aspect). From the combined evaluation of the associated benthic community status and the anthropogenic impacts affecting it, a “high” and “good” environmental status was assessed for five out of the seven studied black forests, with only two forests classified as having a “moderate” and “poor” status, respectively. Overall, our study showed a site-specific variability of mesophotic black coral forest status, explained by different biological community structures and environmental conditions mainly associated with morphological and anthropogenic factors.

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

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

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

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

Responses of the benthic environment to reduction in anthropogenic nutrient loading in the Seto Inland Sea (Japan), based on M-AMBI assessment

Deterioration of the sediment environment and benthic ecosystem is an undesirable effect of eutrophication, but little is known about the response of macrobenthic communities to eutrophication and their long-term recovery. In the present study, temporal changes in benthic ecological status, associated with reductions in anthropogenic impacts on a largest semi-enclosed sea in Japan, were determined using long-term monitoring data from water and sediment quality based on the multivariate AZTI Marine Biotic Index (M-AMBI), focusing on spatial differences in anthropogenic impacts. Several sub-areas were classified based on Chlorophyll a (Chl.a) concentrations in surface water during the 1980s. Chl.a concentrations decreased in all sub-areas except the sub-area with <2 μg Chl.a L^-1 from the 1990s-2010s. On the other hand, total organic carbon contents in sediment decreased and M-AMBI values increased in all sub-areas during this period may be due to reduced lateral organic matter advection from surrounding areas.

Macrofauna community patterns in a Chiloe Island channel used intensely for aquaculture: the ecological status of its benthic environment

Background

It is known that aquaculture may produce negative environmental effects on marine ecosystems. Southern Chile is one of the most important salmon and mussel-producing areas in the world. Here we assess the ecological status of benthic communities near farming centers in Caucahue Channel, Chiloe, which has been used intensely for salmon and mussel production for 30 years.

Methods

The macrofauna, sediments and water column were characterized at distances of 5 to 100 m from three salmon and three mussel-producing centers. Information was also obtained from reference sites 500 to 3000 m from these aquaculture farms. The macrofauna and environmental conditions during winter were analyzed using uni- and multivariate analysis and the AZTI Marine Biotic Index (AMBI) as an indicator of benthic community condition.

Results

(i) There is a high degree of spatial dissimilarity in macrofauna and environmental variables among sampling sites and types of environments (far from or near farming centers) and between the northern and southern areas of the channel; (ii) sediment structure (mean grain size and percentage of total organic matter) correlated with the observed dissimilarities in macrofauna communities; and (iii) the level of perturbation according to AMBI was heterogeneous, with sites in the undisturbed/normal range to moderately disturbed/polluted.

Conclusions

We found a high spatial dissimilarity in benthic macrofauna and environmental variables among sampling sites, environmental types and between the northern and southern areas of the channel. AMBI and multivariate community-environment analysis are useful tools to define the level of perturbation of a geographic area at different spatial scales, using all the ecological information from each sample and replicates.

The Fucales Index: A new tool for monitoring subtidal rocky habitats, and its application to an Atlantic bay subjected to nuclear power plant's effluents

Ecological indices are useful tools for environmental managers to monitor and detect changes caused by natural or anthropogenic disturbances. Despite the fact that descriptors of Fucales species are often included in indices for evaluating changes in coastal marine habitats, there is no index based solely on Fucales abundance. This study proposes the Fucales Index (FI), based on four classes of abundance of a selected Fucales species. The ability of FI to detect changes in the abundance of Sargassum sp. was tested in a Brazilian bay that is subjected to the effluent plume from a nuclear power plant. FI was significantly different when comparing areas inside and outside of the plume area, and it increased with increasing distance from the source of the disturbance. These findings suggest that FI is a suitable tool for assessing the effect of an effluent plume and potentially of other disturbances on rocky shores hosting Fucales.

Quantification of marine benthic communities with metabarcoding

DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomass and abundance from molecular approaches with those from the traditional morphological approach. Abundance and biomass were quantified from 126 samples of benthic intertidal mudflat using traditional morphological approaches and compared with frequency of occurrence and relative read abundance estimates from a molecular approach. A relationship between biomass and relative read abundance was found for two widely dispersed annelid taxa (Pygospio and Scoloplos). None of the other taxons, however, showed such a relationship. We discuss how quantification of abundance and biomass using molecular approaches are hampered by the ecology of DNA i.e. all the processes that determine the amount of DNA in the environment, including the ecology of the benthic species as well as the compositional nature of sequencing data.

Macrobenthic community of a tropical bay system revisited: Historical changes in response to anthropogenic forcing

The present study examines historical perspectives of the macrobenthic community in response to different phases of anthropogenic perturbations in Kakinada Bay, a tropical embayment on the east coast of India. Multivariate analysis of the snapshot data (1958-2017) revealed considerable changes in the Bay environment following a breakwater construction across the Bay mouth in 1997. Subsequently, port expansion activities, industrialization, urbanization, and geomorphic alterations in the Godavari delta brought deterrent changes in the Bay. The fluctuations over the years in hydrographical and sediment characteristics increased environmental heterogeneity and caused significant spatio-temporal shifts in the macrobenthic community between 1995-1996 and 2016-2017. The observed variabilities were suggestive of anthropogenic perturbations of the system with future repercussions on Bay ecosystem functioning. Overall, this study provides evidence on the long-term impact of anthropogenic activities on coastal marine communities and stresses the importance of macrobenthos as bioindicators of such changes in tropical systems.

A review of the classification systems for marine benthic habitats and the new updated Barcelona Convention classification for the Mediterranean

The Mediterranean Sea supports high levels of biodiversity and complexity but is facing increasing human pressures, so that strategies to protect and recover its ecosystems must be a priority in environmental policies. Benthic cartography represents the first step of marine spatial planning for the proper management and protection of our sea. Univocal habitat classification systems are thus needed to map, monitor, and inventory marine habitats, and to guarantee common and shared frames for a harmonized interpretation of the Mediterranean habitat types. In this paper we reviewed the existing classification systems of marine benthic habitats, to discuss the process of revision and updating of one of the first system developed under the Barcelona Convention (BC) in 1998 and adopted by all the Mediterranean countries. The BC classification was revised including the new habitats discovered in the last 30 years, and consistently with the criteria used to revise the EUropean Nature Information System (EUNIS), which is a comprehensive pan-European system for habitat identification. The updated BC classification is hierarchical with 5 levels, which allows representing the most suitable habitat level with respect to the restitution scale of the map. Each habitat is univocally identified by an alpha-numeric code, name and general description following the bionomic approach traditionally adopted in the Mediterranean benthic cartography since the late nineteen century. The new BC classification lists 128 main habitats up to the level 4, which may also contain sub-habitats at the level 5, i.e. associations and facies, totalising 394 habitat types (54% of new habitats with respect to the first BC classification). The updated BC classification system has been used for the selection of reference marine habitats that support two fundamental processes of environmental management: i) identification of Specially Marine Protected Areas according to the SPA/BD Protocol of Barcelona Convention; ii) selection of habitats to be monitored, as requested by the Integrated Monitoring and Assessment Programme and the European Directives (e.g., Water Framework and Marine Strategy). The new list of reference habitats, selected because of their high ecological and conservation value, contains 267 habitats, corresponding to 68% of the total habitats listed in the updated BC classification.

Hematology and Clinical Biochemistry Profiles in Antillean Manatee Trichechus manatus manatus from Different Types of Captivity and Free Living in Northeast Brazil

The Antillean manatee Trichechus manatus manatus can be found along the northern and northeastern coasts of Brazil. Previous studies on the clinical biochemistry of these animals were conducted in North America and the Caribbean, whereas little is known regarding these parameters in South American manatee populations. Accordingly, the objective of the present study was to examine the hematology and clinical biochemistry of Antillean manatees of different sexes and from different environments in northeast Brazil. Whole-blood and serum samples were obtained from healthy individuals. The hemogram analysis was performed and the levels of blood biochemical components were determined using an automated platform. The only statistically significant difference observed in the hemogram was a higher number of heterophils in manatees that were screened during the dry season of the year. Clinical biochemistry profiling revealed that free-ranging manatees presented lower levels of creatinine. Albumin was detected in higher concentrations in animals from rehabilitation captivity, and amylase presented higher levels in manatees that were kept in acclimation captivity. Free-ranging manatees showed higher serum aspartate aminotransferase levels than manatees in rehabilitation captivity. These results can aid veterinarians and conservation professionals in the development of better captive management procedures and in the clinical approach to manatees.

The Benthic Quality Index to Assess Water Quality of Lakes May Be Affected by Confounding Environmental Features

To assess if environmental differences other than water quality may affect the outcome of the Benthic Quality Index, a comparison of the application of four different methods (Benthic Quality Index—BQIES, Lake Habitat Modification Score—LHMS, Lake Habitat Quality Assessment—LHQA and Organisation for Economic Co-operation and Development—OECD) used to classify the lake ecological and hydro-morphological status of 10 Italian lakes was performed. Five lakes were natural and five were reservoirs belonging to both Alpine and Mediterranean Ecoregions. The 10 lakes were sampled using the Water Framework Directive compliant standardized national protocol, which includes sampling soft sediment in the littoral, sublittoral and deep layers along transects with a grab of 225 cm2 during spring and autumn. The application of Generalised Linear Mixed Effect Models both at the lake level and at the single station of each lake highlighted that, at the lake level, no significant correlations existed between any couple of hydro-morphological, ecological and trophic status assessments, with each metric representing a different facet of human impact on the environment. At the single site level, we found significant effects of depth on the metrics of biodiversity. The best approximation of single-site macroinvertebrates diversity among the metrics of overall lake quality was with the LHMS, but not with the BQIES. Our hypotheses that lake macroinvertebrates assemblages depend also on other potential confounding variables of habitat degradation and intrinsic differences between lakes were confirmed, with depth playing a major role. Therefore, the assessment of lakes with different depths may produce different whole-lake BQIES values, only because of the effect of depth gradient and not because of differences in lake quality.

Variables affecting the plankton network in Mediterranean ports

Attention on port waters is increasing since these economically important infrastructures are embedded in the coastal environment and their management needs to be considered in the monitoring programmes of coastal ecosystems. To implement the sustainable development (blue growth) of port areas, a general knowledge on the ongoing processes in their waters needs to be obtained, considering both abiotic and biotic variables. The present study aimed at inspecting the relationships among plankton components to provide insights into the ecology of ports. Seasonal samplings were carried out in three Mediterranean touristic ports where bacterio-, phyto- and zoo-plankton were simultaneously assessed at a large spatial scale and compared with respect to environmental variables and anthropogenic inputs. Factor analysis revealed the effects of load of inland waters, seasonality, water turbulence and hydrocarbon pollution on the planktonic components and zooplankton variability in port sectors characterized by different depths and uses.

Health Evaluation and Risk Factor Identification of Urban Lakes—A Case Study of Lianshi Lake

Health assessment and risk factor identification represent the premise and foundation of scientific management and ecological restoration of urban lakes. Based on in-depth understanding of the nature–society duality of urban lakes, a framework for evaluating urban lake health was constructed, including four modules, namely, establishing an index system; determining the index weight; identifying risk factors; and a comprehensive lake health evaluation. Employing this framework, we evaluated Lianshi Lake, Beijing, classifying the lake condition as “sub-healthy”. Based on the evaluation data, we identified the health risk factors of the lake. We applied standard difference rate (SDR) and risk degree (Rd) (safe degree (Sd)) concepts, and classified the indices of risk areas employing the Pareto analysis method. Finally, we identified the lake residence period, landscape connectivity, and eutrophication as the major risk factors in Lianshi Lake. Three factors constitute the basis of ecosystem health and are key targets of ecological restoration: the lake residence period represents the hydrological and hydrodynamic characteristics of the lake; landscape connectivity is described from an ecological perspective, and represents the integrity of the lake ecosystem; and the eutrophication states describe the water quality characteristics and represent the availability of lake water. The results contribute to decision-making for comprehensive urban lake management.

Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments

Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have applied a prototype version of a phylogenetic microarray to assess the eukaryote community structures of marine sediments from an area with ongoing oil and gas drilling activity. The results were compared with data from both sequencing (metabarcoding) and morphology-based monitoring to evaluate whether microarrays were capable of detecting ecosystem disturbances. A significant correlation between microarray data and chemical pollution indicators, as well as sequencing-based results, was demonstrated, and several potential indicator organisms for pollution-associated parameters were identified, among them a large fraction of microorganisms not covered by traditional morphology-based monitoring. This suggests that microarrays have a potential in future environmental monitoring.

Bioassessment of a Northwest Florida Estuary Using Benthic Macroinvertebrates

Benthic invertebrate community composition was surveyed across the salinity gradient of the Pensacola Bay Estuary in Florida during summer 2016. Macrofauna densities ranged from 1000 to 9300 individuals m^-2 , with highest densities occurring at the upper estuary and the lowest in the mid- and lower estuary. Taxonomic richness and Shannon diversity were lowest in the upper estuary and increased along the salinity gradient. Small-bodied, near-surface infaunal polychaete species (e.g., Mediomastus ambiseta and Paraprionospio alata) dominated the macrofaunal community in fine sediment areas. We calculated the Gulf of Mexico Benthic Index of Biological Integrity for each site and compared the index scores with those from Environmental Monitoring and Assessment Program - Estuaries, an earlier benthic assessment model. Condition evaluations by the different models did not match across all sites in this study; however, scores consistently indicated that most sites were at or near degraded levels, implying that Pensacola Bay represents a marginal habitat for a "healthy" benthic macrofauna community. This study provided new information about the benthic communities and sediments in the Pensacola Bay estuary. Integr Environ Assess Manag 2020;16:245-256. Published 2019. This article is a US Government work and is in the public domain in the USA.

The development of a national approach to monitoring estuarine health based on multivariate analysis

New Zealand has a complex coastal environment spanning a large latitudinal gradient and three water masses. Here we assess whether multivariate analyses of benthic macrofaunal community composition can be a sensitive approach to assessing relative estuarine health across the country, negating the need for regional indices and reducing reliance on reference sites. Community data were used in separate canonical analyses of principal coordinates to create multivariate models of community responses to gradients in mud content and heavy metal contamination. Both models performed well (R² = 0.81, 0.71), and were unaffected by regional and estuarine typology differences. The models demonstrate a sensitive and standardized approach to assessing estuarine health that allowed separation of the two stressors. This approach could be applied to other stressors, countries or regions.

Quantitatively characterizing benthic community-habitat relationships in soft-sediment, nearshore environments to yield useful results for management

Effective management of benthic habitats is important for maintaining heathy and functional aquatic ecosystems. To provide managers with the best possible information, characterizing benthic habitats at the community level is essential; yet, acquiring the data sets needed to achieve this task is resource intensive and, at times, prohibitively expensive. Thus, thoughtful assessments of which data to collect and utilize in benthic habitat characterization studies are needed. Environmental data sets commonly used to characterize benthic habitats include a range of variables from water depth and sediment grain size to seabed features identified by sonar backscatter. The objective of this study was to identify the most useful environmental variables for characterizing infaunal benthic habitats and to determine how to best utilize these variables in analyses (e.g., by comparing continuous vs. categorical explanatory variables). The modeling approach used multivariate regression tree and redundancy analysis along with a critical cross-validation step for model evaluation. Results indicated that models with more than ~7 environmental predictors overfitted the data sets analyzed and that categorizing continuous predictors into categorical ones influenced the proportion of infaunal community variation explained by each model. Habitats identified and characterized on the basis of sonar backscatter explained more of the infaunal community variation than any model that used a combination of other environmental variables (e.g., water depth & sediment grain size) or those constructed using categorical habitat classes from existing classification schemes. We therefore recommend maximizing the potential of sonar-derived variables for characterizing infaunal benthic habitats in nearshore, soft-sediment ecosystems.

Benthic Habitat Morphodynamics-Using Remote Sensing to Quantify Storm-Induced Changes in Nearshore Bathymetry and Surface Sediment Texture at Assateague National Seashore

This study utilizes repeated geoacoustic mapping to quantify the morphodynamic response of the nearshore to storm-induced changes. The aim of this study was to quantitatively map the nearshore zone of Assateague Island National Seashore (ASIS) to determine what changes in bottom geomorphology and benthic habitats are attributable to storm events including hurricane Sandy and the passage of hurricane Joaquin. Specifically, (1) the entire domain of the National Parks Service offshore area was mapped with side-scan sonar and multibeam bathymetry at a resolution comparable to that of the existing pre-storm survey, (2) a subset of the benthic stations were resampled that represented all sediment strata previously identified, and (3) newly obtained data were compared to that from the pre-storm survey to determined changes that could be attributed to specific storms such as Sandy and Joaquin. Capturing event specific dynamics requires rapid response surveys in close temporal association of the before and after period. The time-lapse between the pre-storm surveys for Sandy and our study meant that only a time and storm integrated signature for that storm could be obtained whereas with hurricane Joaquin we could identify impacts to the habitat type and geomorphology more directly related to that particular storm. This storm impacts study provides for the National Park Service direct documentation of storm-related changes in sediments and marine habitats on multiple scales: From large scale, side-scan sonar maps and interpretation of acoustic bottom types, to characterize as fully as possible habitats from 1 to 10 m up to many kilometer scales, as well as from point benthic samples within each sediment stratum and these results can help guide management of the island resources.

Metabarcoding successfully tracks temporal changes in eukaryotic communities in coastal sediments

Metabarcoding is a method that combines high-throughput DNA sequencing and DNA-based identification. Previously, this method has been successfully used to target spatial variation of eukaryote communities in marine sediments, however, the temporal changes in these communities remain understudied. Here, we follow the temporal changes of the eukaryote communities in Baltic Sea surface sediments collected from two coastal localities during three seasons of two consecutive years. Our study reveals that the structure of the sediment eukaryotic ecosystem was primarily driven by annual and seasonal changes in prevailing environmental conditions, whereas spatial variation was a less significant factor in explaining the variance in eukaryotic communities over time. Therefore, our data suggests that shifts in regional climate regime or large-scale changes in the environment are the overdriving factors in shaping the coastal eukaryotic sediment ecosystems rather than small-scale changes in local environmental conditions or heterogeneity in ecosystem structure. More studies targeting temporal changes are needed to further understand the long-term trends in ecosystem stability and response to climate change. Furthermore, this work contributes to the recent efforts in developing metabarcoding applications for environmental biomonitoring, proving a comprehensive option for traditional monitoring approaches.

The Fish Community Index: A Practical Management Tool for Monitoring and Reporting Estuarine Ecological Condition

Indicators of ecological health based on biological communities, including numerous multimetric indices, are used worldwide to assess and report the condition of aquatic ecosystems such as estuaries. Yet, these tools have rarely been applied to support estuary management in Australia. We present a case study of one such multimetric indicator, the Fish Community Index (FCI), which was developed and applied to quantify the ecological condition of estuaries in southwestern Australia (SWA). We outline the rationale, development, and implementation of the FCI for annual monitoring and reporting of the ecological condition of a highly urbanized estuary, highlighting the key research and management outcomes that it has delivered, and evaluating its potential future applications to support estuary management more broadly, both across Australia and internationally. The FCI is founded upon a conceptually simple and scientifically robust rationale and is sensitive to the ecological stressors that affect many estuaries across the region (e.g., hypoxia, algal blooms). Together with an accompanying annual fish monitoring regime, the FCI provides managers with a consistent, robust basis for quantifying and reporting spatiotemporal changes in estuary condition, with easily comprehensible outputs that facilitate communication with stakeholders, ranging from politicians to the general public. We attribute the successful implementation of this management tool to several characteristics, namely 1) support from a long-term, collaborative partnership between managers and researchers; 2) comprehensive testing and validation of the index prior to implementation; 3) a robust, standardized monitoring regime; and 4) sustained resourcing from managers to implement the index as part of a reporting framework. The FCI has also been applied to other SWA estuaries and could provide a platform for more coordinated assessment and reporting of estuarine condition at the bioregional scale, thereby helping to improve the gap in reporting on the biotic integrity of Australian estuaries. Integr Environ Assess Manag 2019;15:726-738. © 2019 SETAC.

The relationship between fish abundance and benthic community structure on artificial reefs in the Mid-Atlantic Bight, and the importance of sea whip corals Leptogorgia virgulata

Autogenic engineers (i.e., biogenic structure) add to habitat complexity by altering the environment by their own physical structures. The presence of autogenic engineers is correlated with increases in species abundance and biodiversity. Biogenic structural communities off the coast of Delaware, Maryland, and Virginia (Delmarva) are comprised of multiple species including boring sponge Cliona celata, various hydroids (i.e., Tubularia sp., Obelia sp., Campanular sp.), northern stone coral Astrangia poculata, sea whips Leptogorgia virgulata, and blue mussels Mytilus edulis. Sea whips are soft corals that provide the majority of vertical height to benthic structure off the coast of the Delmarva peninsula. The mid-Atlantic bight is inhabited by several economically valuable fishes; however, data regarding habitat composition, habitat quality, and fish abundance are scarce. We collected quadrat and sea whip images from 12 artificial reef sites (i.e., shipwrecks) ranging from 10 to 24 m depth to determine proportional coverage of biogenic structures and to assess habitat health, respectively. Underwater video surveys were used to estimate fish abundances on the 12 study sites and determine if fish abundance was related to biogenic coverage and habitat health. Our results showed that higher fish abundance was significantly correlated with higher proportional sea whip coral coverage, but showed no significant relationship to other biogenic structure. Assessment of sea whip condition (as a damage index) showed that sea whip corals on artificial reefs off the Delmarva coast exhibited minor signs of degradation that did not differ significantly among study sites.

Forever young: The successful story of a marine biotic index

In 2000, the AZTI's Marine Biotic Index (AMBI) was published and was one of a number of marine benthic indices development to assess the ecological status of soft-bottom macroinvertebrates. This index, and its derivatives, has been very successful in its application to different geographical areas, across the world, as well as to different environments, from the intertidal to the abyssal, or from tidal freshwater to offshore habitats. In this review, we explain the story behind the AMBI development, and look for an explanation of the index's success. For doing that, we comment on the current practicalities of the index, we present the new AMBI species list, with 9251 taxa, we dismantle six myths around this index, and examine the past and the future of the index. We show that the solid ecological roots of the index make it a robust tool to assess the status of marine benthic communities, at any time and environment. Hence, we think that it will be 'forever young' helping managers in taking informed decisions to improve benthic marine systems.

Benthic quality assessment using M-AMBI in the Seto Inland Sea, Japan

Benthic invertebrates that inhabit the seafloor respond to anthropogenic and natural stresses, and are good indicators for assessing the benthic ecological status. We evaluated the ecosystem health of the Seto Inland Sea based on the multivariate AZTI Marine Biotic Index (M-AMBI), being its first application in a Japanese coastal sea with numerous endemic species. From the 415 locations studied, we were able to use M-AMBI in 384 sites (92.5% in all sites). The result revealed a statistically significant correlation among biotic indices including AMBI, M-AMBI, Richness, and H' (p < 0.01). Most of the physico-chemical parameters of the sediment (water content, total organic carbon (TOC) content, sulfide content, mud content, and oxidation-reduction potential (ORP)) were significantly correlated with each other excluding sediment temperature. The M-AMBI was significantly correlated with physico-chemical variables including water content, TOC content, sulfide content, and ORP. We found that the sites classified into the organically enriched cluster, and having high contents of TOC, mud, and sulfide and negative ORP, corresponded with sites that had significantly low M-AMBI values (bad-poor ecological status). Conversely, sites in the unpolluted sandy cluster were assigned high M-AMBI values (high-good ecological status). Therefore, M-AMBI would be a useful biotic index in Japanese coasts due to the representation of the comprehensive sediment quality.

Coralline algae on hard and soft substrata of a temperate mixed siliciclastic-carbonatic platform: Sensitive assemblages in the Zannone area (western Pontine Archipelago; Tyrrhenian Sea)

In the Mediterranean Sea, coralline algae assemblages (i.e. rhodolith beds and coralligenous assemblages) are considered biodiversity hotspots comparable to tropical reefs. However, information regarding their environmental distribution is still poor. In this view, relevant international actions have been adopted by the European Union to fill this gap. This work represents one of a few cases of predictive (fine-scale) habitats distribution map obtained through an integrated semi-automatic approach based on bathymetry, backscatter, seismic profiles, video, and sampling data. The used method has permitted the identification of nine morphological zones, four backscatter facies, and four benthic habitats distributed on the Zannone seafloor (western Pontine Archipelago; Tyrrhenian Sea). In particular, the finding of widespread sensitive habitats (i.e. coralligenous assemblages and rhodolith beds) reveals as the marine area off the western Pontine Archipelago (Tyrrhenian Sea) is highly suitable for their development (distance from the mainland, lack of river mouths), confirming the relevant ecological value of the Zannone area. Therefore, such information constitutes an update to the Mediterranean habitats distribution inventory, highlighting the need for the application of protection actions possibly targeted in the establishment of a Marine Protected Area.

Anthropogenically enhanced sediment oxygen demand creates mosaic of oxygen deficient zones in the Ganga River: Implications for river health

Dissolved oxygen (DO) plays a major role in sustaining aquatic communities; its concentration and regulatory determinants are considered a key node predicting eutrophy, ecosystem health, and biogeochemical feedbacks. Here we report the status of dissolved oxygen deficit (DOD; hypoxia), and its mechanistic links with sediment oxygen demand (SOD) in the Ganga River. We conducted two independent but interlinked studies during summer low flows of three consecutive years (2016-2018) considering: 1) a 518 km middle segment of the Ganga River between Kanpur upstream and Varanasi downstream; and 2) trajectory analyses downstream two point sources, one flushing industrial effluents (Wazidpur drain) and the other with urban sewage (Assi drain). The concentration of DO at sediment-water interface (DO_sw) did appear < 2.0 mg L^-1 (hypoxia) at Jjmu; and up to 600 m and 800 m downstream Assi and Wazidpur drain respectively. The DOD at sediment-water interface (DOD_sw) was highest at Jjmu and did not show a significant decrease up to 300 m downstream to point sources. The SOD which varied between 2.03 and 13.16 (main river stem); 4.39 and 16.81 (Wazidpur drain); and between 2.00 and 13.50 g O₂ m^-2 d^-1 (Assi drain), was found to be a major contributor of DOD. Principal component analysis (PCA) and non-metric multi-dimensional scaling (NMDS) separated DO and alkaline phosphatase (AP) opposite to oxygen-consuming processes and sediment-P release. Using a dynamic fit model, we tested the dependence of sediment-P release on DO_sw and DOD_sw. A large increase in the sediment-P release with increasing DOD_sw and decreasing DO_sw indicated that the system may compromise its resilience in long-term future in terms of self-fertilization and P-eutrophy if the similar magnitude of anthropogenic pressure is continued. The study advances our understanding towards DOD associated habitat fragmentation, ecosystem resilience and niche opportunities useful for recovery and management of the Ganga River.

Index of biotic integrity based on phytoplankton and water quality index: Do they have a similar pattern on water quality assessment? A study of rivers in Lake Taihu Basin, China

Our study illustrated the ecological conditions in the rivers of Lake Taihu Basin (LTB) using an index of biotic integrity based on phytoplankton (P-IBI), and its performance was compared with the previously developed water quality index (WQI). Samples were collected seasonally at 96 sites covering the major rivers from September 2014 to January 2016. Three critical ecological indices, i.e., phytoplankton density, chlorophyll a (chl a), and Menhinick, were selected from a pool of 22 candidate indices mainly according to the correlations among indices and environmental parameters. The results indicated that the ecological status of LTB based on P-IBI was significantly different at spatial (especially between Tiaoxi and the other 5 river systems) and seasonal scales. Furthermore, the proposed P-IBI effectively identified the major environmental parameters (total nitrogen, ammonium, total phosphorus, and permanganate index) associated with each level (bad, low, and moderate). Moreover, the P-IBI was closely and positively correlated with the WQI at the spatial scale regardless of season. However, the ecological conditions were significantly worse according to the P-IBI at both the spatial (P < 0.001) and seasonal scales (P values of 0.018 in winter and < 0.001 in other seasons, respectively), and the seasonal distribution pattern differed between the two methods. Our study suggests that the P-IBI provides an essential supplement for the assessment of ecological conditions of rivers and that the selected critical indices (phytoplankton density, chl a, and Menhinick) are suitable for river ecosystems. Additionally, compared with WQI, the water quality condition was generally worse when using P-IBI, and this phenomenon requires further attention during water quality assessments, as well as different seasonal distribution patterns.

Techniques for Classifying Seabed Morphology and Composition on a Subtropical-Temperate Continental Shelf

In 2017, the New South Wales (NSW) Office of Environment and Heritage (OEH) initiated a state-wide mapping program, SeaBed NSW, which systematically acquires high-resolution (2–5 m cell size) multibeam echosounder (MBES) and marine LiDAR data along more than 2000 km of the subtropical-to-temperate southeast Australian continental shelf. This program considerably expands upon existing efforts by OEH to date, which have mapped approximately 15% of NSW waters with these technologies. The delivery of high volumes of new data, together with the vast repository of existing data, highlights the need for a standardised, automated approach to classify seabed data. Here we present a methodological approach with new procedures to semi-automate the classification of high-resolution bathymetry and intensity (backscatter and reflectivity) data into a suite of data products including classifications of seabed morphology (landforms) and composition (substrates, habitats, geomorphology). These methodologies are applied to two case study areas representing newer (Wollongong, NSW) and older (South Solitary Islands, NSW) MBES datasets to assess the transferability of classification techniques across input data of varied quality. The suite of seabed classifications produced by this study provide fundamental baseline data on seabed shape, complexity, and composition which will inform regional risk assessments and provide insights into biodiversity and geodiversity.

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

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

Revising the index of watershed integrity national maps

Watersheds provide a range of services valued by society, incorporating biotic and abiotic functions within their boundaries. Recently, an operational definition of watershed integrity was applied and indices of watershed integrity (IWI) and catchment integrity (ICI) were developed and mapped for the conterminous United States. However, these indices were originally derived using equally-weighted first-order approximations of relationships between anthropogenic stressors (obtained from the U.S. EPA's StreamCat dataset) and six watershed functions. In addition, the original calculations of the IWI and ICI did not standardize metrics across these differing scales, resulting in IWI and ICI values that are not directly comparable. We provide an example of how to iteratively update the stressor-watershed function relationships using random forest models and a nationwide response metric representative of one of the six watershed functions. Specifically, we focused on the chemical regulation function (CHEM) of IWI and ICI by relating a composite metric of chemical water quality from 1914 samples to land use metrics explicit to CHEM to refine the nature of these relationships (e.g., non-linear versus linear). The rate of nitrogen fertilizer, agricultural land use, and urban land use were found to be the three most important stressors predicting the national water quality response metric. Revision of CHEM values improved the prediction of several regional- to national-scale water quality indicators. In all cases, exponential decay curves replaced the original negative linear relationship for CHEM. Therefore, the original IWI and ICI values are probably over-estimates of the actual integrity of the Nation's watersheds and catchments. With these revisions, we provide updated national maps of IWI and ICI. The methods outlined here can be implemented iteratively as more and better data become available for all six of the watershed functions to elevate the accuracy and applicability of these indices to various land management issues.

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Adaptation and application of multivariate AMBI (M-AMBI) in US coastal waters

The multivariate AMBI (M-AMBI) is an extension of the AZTI Marine Biotic Index (AMBI) that has been used extensively in Europe, but not in the United States. In a previous study, we adapted AMBI for use in US coastal waters (US AMBI), but saw biases in salinity and score distribution when compared to locally calibrated indices. In this study we modified M-AMBI for US waters and compared its performance to that of US AMBI. Index performance was evaluated in three ways: 1) concordance with local indices presently being used as management tools in three geographic regions of US coastal waters, 2) classification accuracy for sites defined a priori as good or bad and 3) insensitivity to natural environmental gradients. US M-AMBI was highly correlated with all three local indices and removed the compression in response seen in moderately disturbed sites with US AMBI. US M-AMBI and US AMBI did a similar job correctly classifying sites as good or bad in local validation datasets (83 to 100% accuracy vs. 84 to 95%, respectively). US M-AMBI also removed the salinity bias of US AMBI so that lower salinity sites were not more likely to be incorrectly classified as impaired. The US M-AMBI appears to be an acceptable index for comparing condition across broad-scales such as estuarine and coastal waters surveyed by the US EPA's National Coastal Condition Assessment, and may be applicable to areas of the US coast that do not have a locally derived benthic index.

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

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

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.