Benthic Monitoring Research Articles

Developing benthic monitoring programmes to support precise and representative status assessments: a case study from the Baltic Sea

Benthic habitats and communities are key components of the marine ecosystem. Securing their functioning is a central aim in marine environmental management, where monitoring data provide the base for assessing the state of marine ecosystems. In the Baltic Sea, a > 50-year-long tradition of zoobenthic monitoring exists. However, the monitoring programmes were designed prior to the current policies, primarily to detect long-term trends at basin-scale and are thus not optimal to fulfil recent requirements such as area-based periodic status assessments. Here, we review the current monitoring programmes and assess the precision and representativity of the monitoring data in status assessments to identify routes for improvement. At present, the monitoring is focused on soft-bottoms, not accounting for all habitat types occurring in the Baltic Sea. Evaluating the sources of variance in the assessment data revealed that the component accounting for variability among stations forms the largest proportion of the uncertainty. Furthermore, it is shown that the precision of the status estimates can be improved, with the current number of samples. Reducing sampling effort per station, but sampling more stations, is the best option to improve precision in status assessments. Furthermore, by allocating the sampling stations more evenly in the sub-basins, a better representativity of the area can be achieved. However, emphasis on securing the long-term data series is needed if changes to the monitoring programmes are planned.

Influence of benthic currents on cold-water coral habitats: a combined benthic monitoring and 3D photogrammetric investigation

Strong currents are a key component of benthic habitats by supplying food and nutrients to filter-feeding organisms such as cold-water corals. Although field measurements show that cold-water coral habitats exist in areas of elevated bottom currents, flume studies show that cold-water corals feed more effectively at lower flow speeds. This research aims to explore this disconnect in situ by utilising high spatial resolution ROV photogrammetric data coupled with high temporal resolution in situ acoustic doppler current profile measurements at seven study sites within the upper Porcupine Bank Canyon (uPBC), NE Atlantic. Object-based image analysis of photogrammetric data show that coral habitats vary considerably within the upper canyon. Although there is a regional hydrodynamic trend across the uPBC, this variation is likely driven locally by topographic steering. Although live coral tends not to face directly into the prevailing current direction, preferring lower local flows speeds, they can tolerate exposure to high-flow speeds of up to 114 cm s−1, the highest recorded in a Desmophyllum pertusum habitat. Not only do these high flow speeds supply food and nutrients, they may also help contribute to coral rubble production through physical erosion. These results can be incorporated into simulations of future deep-water habitat response to changing environmental conditions while extending the upper current speed threshold for cold-water corals.

Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding.

Since 2010, considerable efforts have been undertaken to monitor the environmental status of European marine waters and ensuring the development of methodological standards for the evaluation of this status. However, the current routine biomonitoring implicates time-consuming and costly manual sorting and morphological identification of benthic macrofauna. Environmental DNA (eDNA) metabarcoding represents an alternative to the traditional monitoring method with very promising results. Here, we tested it further by performing eDNA metabarcoding of benthic eukaryotic communities in the vicinity of two offshore oil and gas platforms in the North Sea. Three different genetic markers (18S V1V2, 18S V9 and COI) were used to assess the environmental pressures induced by the platforms. All markers showed patterns of alpha and beta diversity consistent with morphology-based macrofauna analyses. In particular, the communities' structure inferred from metabarcoding and morphological data significantly changed along distance gradients from the platforms. The impact of the operational discharges was also detected by the variation of biotic index values, AMBI index showing the best correlation between morphological and eDNA data sets. Finally, the sediment physicochemical parameters were used to build a local de novo pressure index that served as benchmark to test the potential of a taxonomy-free approach. Our study demonstrates that metabarcoding approach outperforms morphology-based approach and can be used as a cost and time-saving alternative solution to the traditional morphology-based monitoring in order to monitor more efficiently the impact of industrial activities on marine biodiversity.

Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept.

Monitoring the state of coral reefs is necessary to identify drivers of change and assess effectiveness of management actions. There are several widely-used survey methods, each of which is likely to exhibit different biases that should be quantified if the purpose is to combine datasets obtained via different survey methods. The latter is a particularly important consideration when switching methodologies in long-term monitoring programs and is highly relevant to the Caribbean today. This is because of the continuing need for regionally comparable coral reef monitoring datasets and the fact that the Global Coral Reef Monitoring Network (GCRMN)-Caribbean node is now recommending a photoquadrat (PQ) method over the chain intercept transect method widely adopted by the members of the first truly regional monitoring network, Caribbean Coastal Marine Productivity Program (CARICOMP), in the early-1990s. Barbados, a member of the CARICOMP network, has been using a variation of the chain intercept method in its long-term coral reef monitoring program for more than two decades. Now a member of GCRMN-Caribbean, Barbados is considering switching to the PQ method in conformity with other regional members. Since we expect differences between methods, this study seeks to quantify the nature of those differences to inform Barbados and others considering switching methods. In 2017, both methods were concurrently implemented at 21 permanent monitoring plots across three major reef types in Barbados. Differences in % cover estimates for the six major benthic components, that is, hard corals, sponges, gorgonians, macroalgae, turf algae and crustose coralline algae, were examined within and among reef types. Overall, we found a complex pattern of differences between methods that depended on the benthic component, its relative abundance, and the reef type. We conclude that most benthic components would require a different conversion procedure depending on the reef type, and we provide an example of these procedures for Barbados. The factors that likely contribute to the complex pattern of between-method differences are discussed. Overall, our findings highlight that switching methods will be complicated, but not impossible. Finally, our study fills an important gap by underscoring a promising analytical framework to guide the comparison of ecological survey methods on coral reefs.

Notes on Neorhynchoplax alcocki (Kemp 1917) and Neorhynchoplax demeloi (Kemp 1917) from the Kochi Backwater, India (Crustacea: Decapoda: Brachyura: Hymenosomatidae)

As a part of regular benthic monitoring program in the fragmented brackish-water habitats of Kochi (Cochin), Kerala, India, several specimens of Neorhynchoplax alcocki (Kemp 1917) and Neorhynchoplax demeloi (Kemp 1917) were collected. Description and illustration of male G1 and color shortly after preservation, habitat and its ecological environment are presented for the first time. Key to the Indian species of Neorhynchoplax is provided.

Limited coral mortality following acute thermal stress and widespread bleaching on Palmyra Atoll, central Pacific

During 2015–2016, an El Nino and associated warm water event caused widespread coral bleaching across the equatorial Pacific. Here, we combine 8 yr of benthic monitoring data from permanent photoquadrats with remotely sensed and in situ temperature measurements to assess the impact of the warming event on benthic communities at Palmyra Atoll. We quantified bleaching prevalence across two distinct reef habitats using the best available data. On the fore reef (~ 10 m depth), we quantified bleaching severity within 100–200 m2 large-area plots using the custom visualization and analysis software, Viscore. On the reef terrace (~ 5 m depth), we used 95 focal colonies across three species that have been monitored annually since 2014. The 2015–2016 warm water event was the most extreme such event recorded on Palmyra in the past several decades with a maximum cumulative heat stress (degree heating weeks) of 11.9 °C-weeks. On the fore reef, 90% of live coral cover exhibited some degree of bleaching (32% severe bleaching). On the shallow reef terrace, bleaching was observed in 93% of the focal colonies across all species. Overall, coral cover declined 9% on the fore reef from 2014 to 2017, whereas coral cover did not change on the terrace. These contrasting results may be associated with typical daily temperature ranges on the terrace that are three times greater than on the fore reef. Permanent photoquadrats showed that turf algae initially colonized skeletons of recently dead corals but transitioned to crustose coralline algae within a year. Collectively, our study emphasizes that comprehensive monitoring of benthic communities over time combined with in situ temperature data can provide taxonomically precise trajectories of community change during and following thermal stress.

Spatial properties of sessile benthic organisms and the design of repeat visual survey transects

AbstractMonitoring the impacts of pressures, such as climate change, on marine benthic ecosystems is of high conservation priority. Novel imaging technologies, such as autonomous underwater vehicles (AUVs), remotely operated vehicles (ROVs), and towed systems, now give researchers the ability to monitor benthic ecosystems over large spatial and temporal scales.The design of monitoring programmes that use such technologies is currently hindered by a lack of information about the typical abundance and spatial distributions of target indicators and the level of sampling required to detect changes. A further complicating factor is that these sampling platforms are often not able to be exactly relocated when conducting repeat surveys.How the spatial properties of benthic organisms influence the estimates of cover, given alternative designs that vary in the geolocation precision of transects and the sampling intensity of images, is explored. A geostatistical modelling approach is used to quantify the spatial distribution of 20 key deep‐water invertebrate species at a long‐term monitoring site. The parameter estimates from these models are then used to simulate repeat transects with geolocation error and different levels of sampling.Results suggest that species with short effective ranges (i.e. those with strong spatial dependence over relatively short distances) and large spatial variance, which suggests strong spatial dependence effects, will require greater sampling effort to achieve a given standard of precision.Spatial offsets of 2 m, typical of an AUV, are unlikely to have dramatic impacts on the precision of estimates when sufficient images are sampled, but offsets of 10 m that are typical of towed systems may require a prohibitively high sampling effort for some species. These findings have important implications for benthic monitoring programmes, and highlight the importance of considering the interactions between sampling design, the technical limitations of survey equipment, and the spatial properties of indicator species.

Live-Dead Mismatch of Molluscan Assemblages Indicates Disturbance from Anthropogenic Eutrophication in the Barnegat Bay-Little Egg Harbor Estuary

Previous research combining data on the abundance of benthic invertebrates living in the northernmost section of the Barnegat Bay-Little Egg Harbor estuary with data on water quality suggested a community composition consistent with anthropogenic eutrophication. This part of the estuary, however, experiences both high-nutrient and low-salinity environmental conditions, which are both ecologically stressful to sensitive species and favorable to opportunistic species, complicating assessments of the direct effects of anthropogenic eutrophication. Here, geohistorical baselines were derived from molluscan death assemblages from four localities along a north-south gradient in the bay—two northern low-salinity, high-nutrient sites and two southern high-salinity, low-nutrient sites—to disentangle the effects of salinity and nutrient enrichment on the composition of benthic communities. Disturbance in the northern section of the estuary from freshwater input has been relatively consistent for thousands of years, but nutrient enrichment is a more recent stressor, developing only in the past few decades. The cause of the disturbed benthic community is unlikely to be anthropogenic eutrophication, if there is little discordance between the living and the death assemblage in the northern, low-salinity section of the bay. Comparisons of rank-order abundance (Spearman's rho) and taxonomic similarity (Jaccard-Chao index) of the living and death assemblages along the north-south gradient, however, indicate that compositional shifts occur at the northern sites only. A multivariate index analysis, M-AMBI, which integrates the AZTI Marine Biotic Index, a biotic index based on species sensitivity/tolerance to disturbances, with Shannon diversity and species richness, shows a similar pattern: ecological status shifts (from undisturbed to disturbed) in the northern but not southern sites along the north-south salinity gradient. These independent lines of evidence corroborate the inference that it is most likely anthropogenic eutrophication (and not salinity) disturbance driving observed patterns in benthic community composition. Further sampling and incorporation of geohistorical data into ongoing benthic monitoring in the estuary is recommended to establish ecological baselines where none exist, guide restoration planning, and assess the success of restoration efforts.

The benthic community of the Laurentian Great Lakes: analysis of spatial gradients and temporal trends from 1998-2014.

We used the results of seventeen years of Great Lakes benthic monitoring conducted by the U.S. EPA's Great Lakes National Program Office to describe the spatial and temporal patterns of benthic communities, assess their status, trends, and main drivers, and to infer the potential impact of these community changes on ecosystem functioning. Benthic abundance and diversity were higher at shallow (<70 m in depth) stations with chlorophyll concentrations above 3 μg/L than at deeper sites (<1 μg/L).We infer that lake productivity, measured by chlorophyll was likely the major driver of benthic abundance and diversity across lakes. Consequently, benthic diversity and abundance were the highest in the most productive Lake Erie, followed by lakes Ontario, Michigan, Huron, and Superior. Multivariate analysis distinguished three major communities shared among lakes (littoral, sublittoral, and profundal) that differed in species composition and abundance, functional group diversity, and tolerance to organic pollution. Analysis of temporal trends revealed that the largest changes occurred in profundal communities, apparent in significant shifts in dominant taxa across all lakes except Lake Superior. In lakes Michigan, Huron, and Ontario, the former dominant Diporeia was replaced with Dreissena and Oligochaeta. Profundal species, with the exception of dreissenids, became less abundant, and their depth distribution has shifted. In contrast, density and diversity of native littoral and sublittoral communities increased. The invasion of dreissenids was among the most important drivers of changes in benthic communities. Continued monitoring is critical for tracking unprecedented changes occurring in the Great Lakes ecosystem.

Taxonomy and distribution of Terebellides (Polychaeta: Trichobranchidae) in the northern South China Sea, with description of three new species.

Benthic ecology monitoring in the northern South China Sea revealed many individuals of the polychaete genus Terebellides (Annelida), which are common in soft sediments in shallow waters (4.5-41.0 m). Three new species of Terebellides are described, including T. guangdongensis n. sp., T. yangi n. sp. and T. ectopium n. sp. Terebellides guangdongensis n. sp. is mainly found in Guangdong waters. Terebellides yangi n. sp. and T. ectopium n. sp. are mainly found in Beibu Gulf. A key to all described species of Terebellides from the Northwestern Pacific is given.

Flow velocity–ecology thresholds in Canadian rivers: A comparison of trait and taxonomy‐based approaches

Abstract Understanding the physical and biological mechanisms contributing to flow velocity–ecology relationships is crucial for successful river management. The application of an ecological traits‐based approach offers the potential to explore mechanistic linkages between aquatic communities and a hydrological gradient. To date, however, studies focused on identifying these relationships have been limited by a lack of large‐scale, long‐term biological data. To address this gap at a scale relevant for water policy management, we employed data from a large‐scale standardised benthic monitoring program—the Canadian Aquatic Biomonitoring Network—obtained from wadeable river sites across Canada. We applied the Threshold Indicator Taxa ANalysis method to quantify the response of the macroinvertebrate community, expressed as traditional taxonomic information and also as ecological traits, along a flow velocity gradient in reference and potential reference sites. Five key findings emerged: (1) using taxa and trait modalities revealed different flow velocity thresholds, (2) trait flow velocity indicators were less variable than taxon indicators, especially for positively responding trait modalities, (3) labile and non‐labile trait modalities demonstrated highly similar patterns along the flow velocity gradient, (4) taxa from 12 different orders responded negatively to flow velocity, while only EPT taxa and some dipterans responded positively to flow velocity, and (5) traits related to mobility and ecology (e.g. climber and swimmer habits, preference of cold‐cool eurythermal water and ability to survive desiccation) tended to respond positively to flow velocity, while traits related to morphology, life history and ecology (e.g. sprawler and burrower habits, preference for warm eurythermal water and inability to survive desiccation) tended to respond negatively to flow velocity. Providing ecologically based flow management targets can improve management plans, anticipate ecosystem consequences of anthropogenic change and support the development of policies to mitigate anthropogenic flow alteration. While our taxon and trait modality flow indicators were developed for Canadian watersheds, our methods to develop flow indicators and thresholds are transferrable to other systems where long‐term biomonitoring programs are being developed, underscoring the need for long‐term biomonitoring programs to support better ecosystem management.

Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning.

Monitoring biodiversity is essential to assess the impacts of increasing anthropogenic activities in marine environments. Traditionally, marine biomonitoring involves the sorting and morphological identification of benthic macro-invertebrates, which is time-consuming and taxonomic-expertise demanding. High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) represents a promising alternative for benthic monitoring. However, an important fraction of eDNA sequences remains unassigned or belong to taxa of unknown ecology, which prevent their use for assessing the ecological quality status. Here, we show that supervised machine learning (SML) can be used to build robust predictive models for benthic monitoring, regardless of the taxonomic assignment of eDNA sequences. We tested three SML approaches to assess the environmental impact of marine aquaculture using benthic foraminifera eDNA, a group of unicellular eukaryotes known to be good bioindicators, as features to infer macro-invertebrates based biotic indices. We found similar ecological status as obtained from macro-invertebrates inventories. We argue that SML approaches could overcome and even bypass the cost and time-demanding morpho-taxonomic approaches in future biomonitoring.

First record of the genus Paranebalia Claus, 1880 (Crustacea: Leptostraca) from the Mediterranean Sea

Benthic monitoring of the marine shallow bottoms off Menorca (Balearic Islands, western Mediterranean) has yielded several specimens of the leptostracan genus Paranebalia Claus, 1880. This finding constitutes the first report of the genus from European latitudes and the Mediterranean Sea and therefore the third leptostracan genus known from the Mediterranean. Specimens are described, illustrated and compared to other known species; they might represent a new species but their state of maturity and the lack of an appropriate diagnosis for the type species of the genus, Paranebalia longipes (Willemöes-Suhm, 1875), did not allow to confirm its taxonomic status.

High Resolution Orthomosaics of African Coral Reefs: A Tool for Wide-Scale Benthic Monitoring

Coral reefs play a key role in coastal protection and habitat provision. They are also well known for their recreational value. Attempts to protect these ecosystems have not successfully stopped large-scale degradation. Significant efforts have been made by government and research organizations to ensure that coral reefs are monitored systematically to gain a deeper understanding of the causes, the effects and the extent of threats affecting coral reefs. However, further research is needed to fully understand the importance that sampling design has on coral reef characterization and assessment. This study examines the effect that sampling design has on the estimation of seascape metrics when coupling semi-autonomous underwater vehicles, structure-from-motion photogrammetry techniques and high resolution (0.4 cm) underwater imagery. For this purpose, we use FRAGSTATS v4 to estimate key seascape metrics that enable quantification of the area, density, edge, shape, contagion, interspersion and diversity of sessile organisms for a range of sampling scales (0.5 m × 0.5 m, 2 m × 2 m, 5 m × 5 m, 7 m × 7 m), quadrat densities (from 1–100 quadrats) and sampling strategies (nested vs. random) within a 1655 m2 case study area in Ponta do Ouro Partial Marine Reserve (Mozambique). Results show that the benthic community is rather disaggregated within a rocky matrix; the embedded patches frequently have a small size and a regular shape; and the population is highly represented by soft corals. The genus Acropora is the more frequent and shows bigger colonies in the group of hard corals. Each of the seascape metrics has specific requirements of the sampling scale and quadrat density for robust estimation. Overall, the majority of the metrics were accurately identified by sampling scales equal to or coarser than 5 m × 5 m and quadrat densities equal to or larger than 30. The study indicates that special attention needs to be dedicated to the design of coral reef monitoring programmes, with decisions being based on the seascape metrics and statistics being determined. The results presented here are representative of the eastern South Africa coral reefs and are expected to be transferable to coral reefs with similar characteristics. The work presented here is limited to one study site and further research is required to confirm the findings.

Benefits and shortcomings of non-destructive benthic imagery for monitoring hard-bottom habitats

Hard-bottom habitats with complex topography and fragile epibenthic communities are still not adequately considered in benthic monitoring programs, despite their potential ecological importance. While indicators of ecosystem health are defined by major EU directives, methods commonly used to measure them are deficient in quantification of biota on hard surfaces. We address the suitability of seafloor imaging for monitoring activities. We compared the ability of high-resolution imagery and physical sampling methods (grab, dredge, SCUBA-diving) to detect taxonomic and functional components of epibenthos. Results reveal that (1) with minimal habitat disturbance on large spatial scales, imagery provides valuable, cost-effective assessment of rocky reef habitat features and community structure, (2) despite poor taxonomic resolution, image-derived data for habitat-forming taxa might be sufficient to infer richness of small sessile and mobile fauna, (3) physical collections are necessary to develop a robust record of species richness, including species-level taxonomic identifications, and to establish a baseline.

Temporal and spatial variability in the cover of deep reef species: Implications for monitoring

Imagery collected from Autonomous Underwater Vehicles (AUVs) provides a novel means of monitoring changes in benthic ecosystems over large spatial scales and depth ranges. However, for many benthic ecosystems there is little baseline data to quantify temporal and spatial variance for key indicator species. This information is crucial for isolating background “noise” from long-term “signals”. Here we quantify components of variance for five key deep-water sessile invertebrate species across four long-term benthic monitoring sites in a region undergoing strong climate-driven changes. We use linear mixed models to estimate the contribution of sources of spatial and temporal variance in species covers from empirical data. We then combine this information with projected long-term climate-driven changes in the cover of these groups and test the power of various survey designs to detect change through time. Large short-term temporal and spatial variability in the cover of a gorgonian octocoral results in high components of variance that limit the detectability of the projected long-term trend for this species. Conversely, for three of the sponge species high power is achievable with revisits to the four original sites every two years until 2060. By including more sites in the revisit design, high power can be achieved with less frequent revisits. For the fifth species, we find high power is unachievable due to the small trend predicted. Overall, we highlight how examination of components of variance in a system can aid in the selection of suitable indicators and the establishment of effective monitoring programs.

Building a database for long-term monitoring of benthic macrofauna in the Pertuis-Charentais (2004-2014).

BackgroundLong-term benthic monitoring is rewarding in terms of science, but labour-intensive, whether in the field, the laboratory, or behind the computer. Building and managing databases require multiple skills, including consistency over time as well as organisation via a systematic approach. Here, we introduce and share our spatially explicit benthic database, comprising 11 years of benthic data. It is the result of intensive benthic sampling that has been conducted on a regular grid (259 stations) covering the intertidal mudflats of the Pertuis-Charentais (Marennes-Oléron Bay and Aiguillon Bay). Samples were taken by foot or by boats during winter depending on tidal height, from December 2003 to February 2014. The present dataset includes abundances and biomass densities of all mollusc species of the study regions and principal polychaetes as well as their length, accessibility to shorebirds, energy content and shell mass when appropriate and available. This database has supported many studies dealing with the spatial distribution of benthic invertebrates and temporal variations in food resources for shorebird species as well as latitudinal comparisons with other databases. In this paper, we introduce our benthos monitoring, share our data, and present a "guide of good practices" for building, cleaning and using it efficiently, providing examples of results with associated R code.New informationThe dataset has been formatted into a geo-referenced relational database, using PostgreSQL open-source DBMS. We provide density information, measurements, energy content and accessibility of thirteen bivalve, nine gastropod and two polychaete taxa (a total of 66,620 individuals)​ for 11 consecutive winters. Figures and maps are provided to describe how the dataset was built, cleaned, and how it can be used. This dataset can again support studies concerning spatial and temporal variations in species abundance, interspecific interactions as well as evaluations of the availability of food resources for small- and medium size shorebirds and, potentially, conservation and impact assessment studies.

Identifying relevant scales of variability for monitoring epifaunal reef communities at a tidal energy extraction site

The SeaGen tidal energy turbine is located in the Strangford Narrows, Northern Ireland. The Narrows are designated as a Natura 2000 site, host unique biological assemblages and exhibit very high tidal velocities.This study describes an asymmetrical BACI design monitoring program that was aimed at assessing the potential impact the SeaGen may have on epifaunal boulder reef communities. This study presents a novel methodology for monitoring epifaunal communities within highly variable and poorly understood tidal rapid environments.We identify bare rock as a key measure of disturbance within tidal energy extraction sites and propose a new successional model for epifaunal reef communities on subtidal stable substrates. We also present an Ecological Quality Ratio (EQR); the High Energy Hard Substrate (HEHS) index for use in monitoring programs within tidal energy extraction sites.Seasonality significantly affected epifaunal community structure, bare rock distributions and EQR values at all stations equally over time. SeaGen is not significantly affecting epifaunal community structure, bare rock distributions or EQR values at the impact site. The HEHS index has the potential to standardise benthic monitoring in tidal energy extraction sites.

Can diver operated stereo-video surveys for fish be used to collect meaningful data on benthic coral reef communities?

Information for monitoring marine communities is increasingly collected using digital imagery and there is a need to understand how data collected using different methods compare. This study investigated the comparability of benthic data collected by downward facing diver operated stereo-video (DOV) with a forward facing stereo-DOV typically used in fish surveys. Data sets were collected by both methods from the same transect along which the benthos visible in each method was identified by taxonomy, growth form or substratum class. Analyses indicated that 77% of taxa were identified by both methods however, forward facing-DOV recorded 35 genera and downward-DOV 43 genera and there were significant (p < 0.05) differences in the percent cover of dominant benthic categories. The forward facing stereo-DOV detected significantly more vertically erect coral (∼ 10%), specifically branching genera Acropora, Echinopora, and Porites, and canopy forming algae, Sargassum spp., but proportionally less turf algae (∼ 20%) than the downward facing video. Cost-benefit optimization indicated that the forward facing video was more cost-effective at detecting broad scale change in coral, but less effective at detecting change in non-canopy forming algae compared to the downward video. Despite differences in detection of coral and algae, Deming regression analysis detected significant relationships between the percentages of common benthos recorded by both methods, enabling direct comparison between the data collected by each method at a broad scale level and for common benthos. Stereo-DOV surveys for fish can be considered a potential technique for the description of reef benthos that captures key elements of structural complexity, but is not necessarily suitable for taxonomic benthic monitoring.

Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

The rapid growth of the salmon industry necessitates the development of fast and accurate tools to assess its environmental impact. Macrobenthic monitoring is commonly used to measure the impact of organic enrichment associated with salmon farm activities. However, clas- sical benthic monitoring can hardly answer the rapidly growing demand because the morpholog- ical identification of macro-invertebrates is time-consuming, expensive and requires taxonomic expertise. Environmental DNA (eDNA) metabarcoding of meiofauna-sized organisms, such as Foraminifera, was proposed to overcome the drawbacks of macrofauna-based benthic monitoring. Here, we tested the application of foraminiferal metabarcoding to benthic monitoring of salmon farms in Norway. We analysed 140 samples of eDNA and environmental RNA (eRNA) extracted from surface sediment samples collected at 4 salmon farming sites in Norway. We sequenced the variable region 37f of the 18S rRNA gene specific to Foraminifera. We compared our data to the results of macrofaunal surveys of the same sites and tested the congruence between various diver- sity indices inferred from metabarcoding and morphological data. The results of our study confirm the usefulness of Foraminifera as bioindicators of organic enrichment associated with salmon farming. The foraminiferal diversity increased with the distance to fish cages, and metabarcoding provides an assessment of the ecological quality comparable to the morphological analyses. The foraminiferal metabarcoding approach appears to be a promising alternative to classical benthic monitoring, providing a solution to the morpho-taxonomic bottleneck of macrofaunal surveys.