Integrating time-series hydroacoustics and video observations for detecting changes in benthic habitats

The ability to quantify change in marine benthic habitats must be considered a key goal of marine habitat mapping activities. Changes in distribution of distinct suites of benthic biological species may occur as a result of natural or human induced processes and these processes may operate at a range of temporal and spatial scales. It is important to understand natural small scale inter-annual patterns of change in order to separate these signals from potential patterns of longer term change. Work to describe these processes of change from an acoustic remote sensing stand point has thus far been limited due to the relatively recent availability of full coverage swath acoustic datasets and cost pressures associated with multiple surveys of the same area. This paper describes the use of landscape transition analysis as a means to differentiate seemingly random patterns of habitat change from systematic signals of habitat transition at a shallow (10–50 m depth) 18 km2 study area on the temperate Australian continental shelf between the years 2006 and 2007. Supervised classifications for each year were accomplished using independently collected high resolution (3 m cell-size) multibeam echosounder (MBES) and video-derived reference data. Of the 4 representative biotic classes considered, signals of directional systematic changes were observed to occur between a shallow kelp dominated class, a deep sessile invertebrate dominated class and a mixed class of kelp and sessile invertebrates. These signals of change are interpreted as inter-annual variation in the density and depth related extent of canopy forming kelp species at the site, a phenomenon reported in smaller scale temporal studies of the same species. The methods applied in this study provide a detailed analysis of the various components of the traditional change detection cross tabulation matrix allowing identification of the strongest signals of systematic habitat transitions across broad geographical regions. Identifying clear patterns of habitat change is an important first step in linking these patterns to the processes that drive them.

Detecting patterns of change in benthic habitats by acoustic remote sensing

Changes in benthic habitats occur as a result of natural variation or human-induced processes. It is important to understand natural fine-scale inter-annual patterns of change to separate these signals from patterns of long-term change. Describing change from an acoustic remote sensing standpoint has been facilitated by the recent availability of full coverage swath acoustic datasets, but is limited by cost pressures associated with multiple surveys of the same area. We studied the use of landscape transition analysis as a means to differentiate seemingly random patterns of habitat change from systematic signals of habitat transition at a shallow (10 to 50 m depth) 18 km2 site on the temperate Australian continental shelf in 2006 and 2007. Supervised classifications for each year were accomplished using inde pendently collected highresolution swath acoustic and video reference data. Of the 4 representative biotic clas ses considered, signals of directional systematic changes occurred be tween a kelp-dominated class, a sessile invertebrate-dominated class and a mixed class of kelp and sessile invertebrates. We provide a detailed analysis of the components of the traditional change detection cross tabulation matrix, allowing identification of the strongest signals of systematic habitat transitions. Iden tifying patterns of habitat change is an important first step toward understanding the processes that drive them.

Climate-Driven Range Shifts Within Benthic Habitats Across a Marine Biogeographic Transition Zone.

Anthropogenic climate change is causing unprecedented rapid responses in marine communities, with species across many different taxonomic groups showing faster shifts in biogeographic ranges than in any other ecosystem. Spatial and temporal trends for many marine species are difficult to quantify, however, due to the lack of long-term datasets across complete geographical distributions and the occurrence of small-scale variability from both natural and anthropogenic drivers. Understanding these changes requires a multidisciplinary approach to bring together patterns identified within long-term datasets and the processes driving those patterns using biologically relevant mechanistic information to accurately attribute cause and effect. This must include likely future biological responses, and detection of the underlying mechanisms in order to scale up from the organismal level to determine how communities and ecosystems are likely to respond across a range of future climate change scenarios. Using this multidisciplinary approach will improve the use of robust science to inform the development of fit-for-purpose policy to effectively manage marine environments in this rapidly changing world.

Climate-Driven Range Shifts Within Benthic Habitats Across a Marine Biogeographic Transition Zone.

Anthropogenic climate change is causing unprecedented rapid responses in marine communities, with species across many different taxonomic groups showing faster shifts in biogeographic ranges than in any other ecosystem. Spatial and temporal trends for many marine species are difficult to quantify, however, due to the lack of long-term datasets across complete geographical distributions and the occurrence of small-scale variability from both natural and anthropogenic drivers. Understanding these changes requires a multidisciplinary approach to bring together patterns identified within long-term datasets and the processes driving those patterns using biologically relevant mechanistic information to accurately attribute cause and effect. This must include likely future biological responses, and detection of the underlying mechanisms in order to scale up from the organismal level to determine how communities and ecosystems are likely to respond across a range of future climate change scenarios. Using this multidisciplinary approach will improve the use of robust science to inform the development of fit-for-purpose policy to effectively manage marine environments in this rapidly changing world.

Mapping and characterisation of the inter-reefal benthic assemblages of the Torres Strait

A comprehensive survey of the benthic assemblages of the Torres Strait was conducted in order to provide critical baseline information for regional marine planning, assessing the environmental sustainability of fisheries and understanding the ecosystems of the region. Over 150 sites throughout the region were sampled with a modified prawn trawl, towed underwater video, pipe dredge and epibenthic sled. This manuscript provides a broad overview of the activities undertaken and data collected. Two thousand three hundred and seventy-two different nominal species were sampled by the trawl and sled, only 728 by both gears. The towed video was not able to provide the same level of taxonomic resolution of epibenthic taxa, but was particularly useful in areas where the seabed was too rough to be sampled. Data from the trawl, sled and video were combined to characterise the epibenthic assemblages of the region. Data from the towed video was also used to provide a characterisation of the inter-reefal benthic habitats, which was then analysed in combination with physical covariate data to examine relationships between the two. Levels of mud and gravel in the sediments, trawling effort and seabed current stress were the covariates most significantly correlated with the nature of the seabed habitats.

Long-Term Monitoring of Ecological Conditions In Gray’s Reef National Marine Sanctuary: Comparison of soft-bottom benthic assemblages and contaminant levels in sediments and biota in Spring 2000 and 2005

As part of an ongoing program of benthic sampling and related assessments of sediment quality at Gray’s Reef National Marine Sanctuary (GRNMS) off the coast of Georgia, a survey of soft-bottom benthic habitats was conducted in spring 2005 to characterize condition of macroinfaunal assemblages and levels of chemical contaminants in sediments and biota relative to a baseline survey carried out in spring 2000. Distribution and abundance of macrobenthos were related foremost to sediment type (median particle size, % gravel), which in turn varied according to bottom-habitat mesoscale features (e.g., association with live bottom versus flat or rippled sand areas). Overall abundance and diversity of soft-bottom benthic communities were similar between the two years, though dominance patterns and relative abundances of component species were less repeatable. Seasonal summer pulses of a few taxa (e.g., the bivalve Ervilia sp. A) observed in 2000 were not observed in 2005. Concentrations of chemical contaminants in sediments and biota, though detectable in both years, were consistently at low, background levels and no exceedances of sediment probable bioeffect levels or FDA action levels for edible fish or shellfish were observed. Near-bottom dissolved oxygen levels and organic-matter content of sediments also have remained within normal ranges. Highly diverse benthic assemblages were found in both years, supporting the premise that GRNMS serves as an important reservoir of marine biodiversity. A total of 353 taxa (219 identified to species) were collected during the spring 2005 survey. Cumulatively, 588 taxa (371 identified to species) have been recorded in the sanctuary from surveys in 2000, 2001, 2002, and 2005. Species Accumulation Curves indicate that the theoretical maximum should be in excess of 600 species. Results of this study will be of value in advancing strategic science and management goals for GRNMS, including characterization and long-term monitoring of sanctuary resources and processes, as well as supporting evolving interests in ecosystem-based management of the surrounding South Atlantic Bight (SAB) ecosystem. (PDF contains 46 pages)

Detecting fish aggregations from reef habitats mapped with high resolution side scan sonar imagery

As part of a multibeam and side scan sonar (SSS) benthic survey of the Marine Conservation District (MCD) south of St. Thomas, USVI and the seasonal closed areas in St. Croix—Lang Bank (LB) for red hind (Epinephelus guttatus) and the Mutton Snapper (MS) (Lutjanus analis) area—we extracted signals from water column targets that represent individual and aggregated fish over various benthic habitats encountered in the SSS imagery. The survey covered a total of 18 km2 throughout the federal jurisdiction fishery management areas. The complementary set of 28 habitat classification digital maps covered a total of 5,462.3 ha; MCDW (West) accounted for 45% of that area, and MCDE (East) 26%, LB 17%, and MS the remaining 13%. With the exception of MS, corals and gorgonians on consolidated habitats were significantly more abundant than submerged aquatic vegetation (SAV) on unconsolidated sediments or unconsolidated sediments. Continuous coral habitat was the most abundant consolidated habitat for both MCDW and MCDE (41% and 43% respectively). Consolidated habitats in LB and MS predominantly consisted of gorgonian plain habitat with 95% and 83% respectively. Coral limestone habitat was more abundant than coral patch habitat; it was found near the shelf break in MS, MCDW, and MCDE. Coral limestone and coral patch habitats only covered LB minimally. The high spatial resolution (0.15 m) of the acquired imagery allowed the detection of differing fish aggregation (FA) types. The largest FA densities were located at MCDW and MCDE over coral communities that occupy up to 70% of the bottom cover. Counts of unidentified swimming objects (USOs), likely representing individual fish, were similar among locations and occurred primarily over sand and shelf edge areas. Fish aggregation school sizes were significantly smaller at MS than the other three locations (MCDW, MCDE, and LB). This study shows the advantages of utilizing SSS in determining fish distributions and density.

Integration of fisheries acoustics surveys and bathymetric mapping to characterize midwater-seafloor habitats of US Virgin Islands and Puerto Rico (2008-2010)

NOAA’s Coral Reef Conservation program (CRCP) develops coral reef management priorities by bringing together various partners to better understand threats to coral reef ecosystems with the goal of conserving, protecting and restoring these resources. Place-based and ecosystem-based management approaches employed by CRCP require that spatially explicit information about benthic habitats and fish utilization are available to characterize coral reef ecosystems and set conservation priorities. To accomplish this, seafloor habitat mapping of coral reefs around the U.S. Virgin Islands (USVI) and Puerto Rico has been ongoing since 2004. In 2008, fishery acoustics surveys were added to NOAA survey missions in the USVI and Puerto Rico to assess fish distribution and abundance in relation to benthic habitats in high priority conservation areas. NOAA’s National Centers for Coastal Ocean Science (NCCOS) have developed fisheries acoustics survey capabilities onboard the NOAA ship Nancy Foster to complement the CRCP seafloor habitat mapping effort spearheaded by the Center for Coastal Monitoring and Assessment Biogeography Branch (CCMA-BB). The integration of these activities has evolved on the Nancy Foster over the three years summarized in this report. A strategy for improved operations and products has emerged over that time. Not only has the concurrent operation of multibeam and fisheries acoustics surveys been beneficial in terms of optimizing ship time and resources, this joint effort has advanced an integrated approach to characterizing bottom and mid-water habitats and the fishes associated with them. CCMA conducts multibeam surveys to systematically map and characterize coral reef ecosystems, resulting in products such as high resolution bathymetric maps, backscatter information, and benthic habitat classification maps. These products focus on benthic features and live bottom habitats associated with them. NCCOS Centers (the Center for Coastal Fisheries and Habitat Research and the Center for Coastal Environmental Health and Biomolecular Research) characterize coral reef ecosystems by using fisheries acoustics methods to capture biological information through the entire water column. Spatially-explicit information on marine resources derived from fisheries acoustics surveys, such as maps of fish density, supports marine spatial planning strategies and decision making by providing a biological metric for evaluating coral reef ecosystems and assessing impacts from pollution, fishing pressure, and climate change. Data from fisheries acoustics surveys address management needs by providing a measure of biomass in management areas, detecting spatial and temporal responses in distribution relative to natural and anthropogenic impacts, and identifying hotspots that support high fish abundance or fish aggregations. Fisheries acoustics surveys conducted alongside multibeam mapping efforts inherently couple water column data with information on benthic habitats and provide information on the heterogeneity of both benthic habitats and biota in the water column. Building on this information serves to inform resource managers regarding how fishes are organized around habitat structure and the scale at which these relationships are important. Where resource managers require place-based assessments regarding the location of critical habitats along with high abundances of fish, concurrent multibeam and fisheries acoustics surveys serve as an important tool for characterizing and prioritizing coral reef ecosystems. This report summarizes the evolution of fisheries acoustics surveys onboard the NOAA ship Nancy Foster from 2008 to 2010, in conjunction with multibeam data collection, aimed at characterizing benthic and mid-water habitats in high priority conservation areas around the USVI and Puerto Rico. It also serves as a resource for the continued development of consistent data products derived from acoustic surveys. By focusing on the activities of 2010, this report highlights the progress made to date and illustrates the potential application of fisheries data derived from acoustic surveys to the management of coral reef ecosystems.

A surveillance strategy for invasive species of concern in deepwater habitats of the Northwestern Hawaiian Islands

This report describes a surveillance strategy to detect deepwater invasive species in the Northwestern Hawaiian Islands. A need for this strategy was identified in the Papahānaumokuākea Marine National Monument Management Plan and the Monument’s Draft Natural Resources Science Plan. This strategy focuses on detecting two species of concern, the octocoral Carijoa riisei and the red alga Hypnea musciformis. Most research on invasive species in the Hawaiian archipelago has focused on shallow water habitats within the limits of conventional SCUBA (0-30 m). Deeper habitats such as mesophotic reefs are much more difficult to access and consequently little is known about the distribution of deepwater invasive species or their impacts. Recent deepwater (>30 m) sightings of H. musciformis and C. riisei, in and near NWHI, respectively, have prompted a call for further research and surveillance of invasive species in deepwater habitats. This report compiles the most up to date information about these two species of concern in deepwater habitats. A literature search and conversations with subject matter experts was used to identify their current distribution, preferred habitat types, optimal detection methods and ways to efficiently sample the vast extent of NWHI. The proposed sampling strategy prioritizes survey effort where C. riisei and H. musciformis are most likely to be found. At coarse spatial scales (tens to hundreds of kilometers), opportunistic observations and distance from the Main Hawaiian Islands, a principal propagule source, are used to identify high-risk islands and banks. At fine spatial scales (meters to tens of kilometers) a habitat suitability model was developed to identify high-risk habitats. The habitat suitability model focused on habitat preferences of C. riisei, since the species is well studied and adequate data exists to map habitats. There was insufficient information to identify suitable habitat for H. muscifomis. Habitat preferences for the algae are poorly understood and there is a lack of data at relevant spatial scales to map those preferences which are known. The principal habitats identified by the habitat suitability model were ledges and the edges of rugose coral reefs, where the shade loving octocoral would likely be found. Habitat suitability maps were developed for seven atolls and banks to aid in survey site selection. The protocol relied on technical divers to conduct visual surveys of benthic habitats. It was developed to increase the efficiency of surveys, maximize the probability of detection, identify important information relevant to future surveys and standardize results. The strategy, model and protocol were tested during a field mission in 2009 at several atolls and islands in NWHI. The field mission did not detect any invasive species among deepwater habitats and much was learned to improve future surveys. Data gaps and improvements are discussed.

Biogeographic characterization of essential fish habitats affected by human activities in the coastal zone of Puerto Rico

The overall purpose of this project was to collect available information on the characteristics of essential fish habitats in protected and non-protected marine areas around the islands of Puerto Rico. Specifically, this project compiled historical information on benthic habitats and the status of marine resources into a Geographic Information System (GIS) by digitizing paper copies of existing marine geologic maps that were developed for the Caribbean Fishery Management Council (CFMC) for areas around the Commonwealth of Puerto Rico. In addition, information on benthic habitat types, Essential Fish Habitat (EFH) requirements, and fishing and non-fishing impacts to marine resources were compiled for two priority areas: La Parguera and Vieques. The information obtained will help to characterize and select habitats for future monitoring of impacts of fishing and non-fishing activities and to develop management recommendations for conservation of important marine habitats. The project focused specifically on areas identified as priorities for conservation by the Puerto Rico Department of Natural and Environmental Resources (DNER) and the Local Action Strategy Overfishing Group.

The potential use of mapped extent and distribution of habitats as indicators of Good Environmental Status (GES)

The Healthy and Biologically Diverse Seas Evidence Group (HBDSEG) has been tasked with providing the technical advice for the implementation of the Marine Strategy Framework Directive (MSFD) with respect to descriptors linked to biodiversity. A workshop was held in London to address one of the Research and Development (R&D) proposals entitled: ‘Mapping the extent and distribution of habitats using acoustic and remote techniques, relevant to indicators for area/extent/habitat loss.’ The aim of the workshop was to identify, define and assess the feasibility of potential indicators of benthic habitat distribution and extent, and identify the R&D work which could be required to fully develop these indicators. The main points that came out of the workshop were: (i) There are many technical aspects of marine habitat mapping that still need to be resolved if cost-effective spatial indicators are to be developed. Many of the technical aspects that need addressing surround issues of consistency, confidence and repeatability. These areas should be tackled by the JNCC Habitat Mapping and Classification Working Group and the HBDSEG Seabed Mapping Working Group. (ii) There is a need for benthic ecologists (through the HBDSEG Benthic Habitats Subgroup and the JNCC Marine Indicators Group) to finalise the list of habitats for which extent and/or distribution indicators should be considered for development, building upon the recommendations from this report. When reviewing the list of indicators, benthic habitats could also be distinguished into those habitats that are defined/determined primarily by physical parameters (although including biological assemblages) (e.g. subtidal shallow sand) and those defined primarily by their biological assemblage (e.g. seagrass beds). This distinction is important as some anthropogenic pressures may influence the biological component of the ecosystem despite not having a quantifiable effect on the physical habitat distribution/extent. (iii) The scale and variety of UK benthic habitats makes any attempt to undertake comprehensive direct mapping exercises prohibitively expensive (especially where there is a need for repeat surveys for assessment). There is a clear need therefore to develop a risk-based approach that uses indirect indicators (e.g. modelling), such as habitats at risk from pressures caused by current human activities, to develop priorities for information gathering. The next steps that came out of the workshop were: (i) A combined approach should be developed by the JNCC Marine Indicators Group together with the HBDSEG Benthic Habitats Subgroup, which will compile and ultimately synthesise all the criteria used by the three different groups from the workshop. The agreed combined approach will be used to undertake a final review of the habitats considered during the workshop, and to evaluate any remaining habitats in order to produce a list of habitats for indicator development for which extent and/or distribution indicators could be appropriate. (ii) The points of advice raised at this workshop, alongside the combined approach aforementioned, and the final list of habitats for extent and/or distribution indicator development will be used to develop a prioritised list of actions to inform the next round of R&D proposals for benthic habitat indicator development in 2014. This will be done through technical discussions within JNCC and the relevant HBDSEG Subgroups. The preparation of recommendations by these groups should take into account existing work programmes, and consider the limited resources available to undertake any further R&D work.

Hydro-acoustic remote sensing of benthic biological communities on the shallow South East Australian continental shelf

Information regarding the composition and extent of benthic habitats on the South East Australian continental shelf is limited. In this habitat mapping study, multibeam echosounder (MBES) data are integrated with precisely geo-referenced video ground-truth data to quantify benthic biotic communities at Cape Nelson, Victoria, Australia. Using an automated decision tree classification approach, 5 representative biotic groups defined from video analysis were related to hydro-acoustically derived variables in the Cape Nelson survey area. Using a combination of multibeam bathymetry, backscatter and derivative products produced highest overall accuracy (87%) and kappa statistic (0.83). This study demonstrates that decision tree classifiers are capable of integrating variable data types for mapping distributions of benthic biological assemblages, which are important in maintaining biodiversity and other system services in the marine environment.

Comparison of automated classification techniques for predicting benthic biological communities using hydroacoustics and video observations

The effective management of our marine ecosystems requires the capability to identify, characterise and predict the distribution of benthic biological communities within the overall seascape architecture. The rapid expansion of seabed mapping studies has seen an increase in the application of automated classification techniques to efficiently map benthic habitats, and the need of techniques to assess confidence of model outputs. We use towed video observations and 11 seafloor complexity variables derived from multibeam echosounder (MBES) bathymetry and backscatter to predict the distribution of 8 dominant benthic biological communities in a 54 km² site, off the central coast of Victoria, Australia. The same training and evaluation datasets were used to compare the accuracies of a Maximum Likelihood Classifier (MLC) and two new generation decision tree methods, QUEST (Quick Unbiased Efficient Statistical Tree) and CRUISE (Classification Rule with Unbiased Interaction Selection and Estimation), for predicting dominant biological communities. The QUEST classifier produced significantly better results than CRUISE and MLC model runs, with an overall accuracy of 80% (Kappa 0.75). We found that the level of accuracy with the size of training set varies for different algorithms. The QUEST results generally increased in a linear fashion, CRUISE performed well with smaller training data sets, and MLC performed least favourably overall, generating anomalous results with changes to training size. We also demonstrate how predicted habitat maps can provide insights into habitat spatial complexity on the continental shelf. Significant variation between patch-size and habitat types and significant correlations between patch size and depth were also observed.

Integrating multibeam backscatter angular response, mosaic and bathymetry data for benthic habitat mapping

Multibeam echosounders (MBES) are increasingly becoming the tool of choice for marine habitat mapping applications. In turn, the rapid expansion of habitat mapping studies has resulted in a need for automated classification techniques to efficiently map benthic habitats, assess confidence in model outputs, and evaluate the importance of variables driving the patterns observed. The benthic habitat characterisation process often involves the analysis of MBES bathymetry, backscatter mosaic or angular response with observation data providing ground truth. However, studies that make use of the full range of MBES outputs within a single classification process are limited. We present an approach that integrates backscatter angular response with MBES bathymetry, backscatter mosaic and their derivatives in a classification process using a Random Forests (RF) machine-learning algorithm to predict the distribution of benthic biological habitats. This approach includes a method of deriving statistical features from backscatter angular response curves created from MBES data collated within homogeneous regions of a backscatter mosaic. Using the RF algorithm we assess the relative importance of each variable in order to optimise the classification process and simplify models applied. The results showed that the inclusion of the angular response features in the classification process improved the accuracy of the final habitat maps from 88.5% to 93.6%. The RF algorithm identified bathymetry and the angular response mean as the two most important predictors. However, the highest classification rates were only obtained after incorporating additional features derived from bathymetry and the backscatter mosaic. The angular response features were found to be more important to the classification process compared to the backscatter mosaic features. This analysis indicates that integrating angular response information with bathymetry and the backscatter mosaic, along with their derivatives, constitutes an important improvement for studying the distribution of benthic habitats, which is necessary for effective marine spatial planning and resource management.

Wave exposure as a predictor of benthic habitat distribution on high energy temperate reefs

The new found ability to measure physical attributes of the marine environment at high resolution across broad spatial scales has driven the rapid evolution of benthic habitat mapping as a field in its own right. Improvement of the resolution and ecological validity of seafloor habitat distribution models has, for the most part, paralleled developments in new generations of acoustic survey tools such as multibeam echosounders. While sonar methods have been well demonstrated to provide useful proxies of the relatively static geophysical patterns that reflect distribution of benthic species and assemblages, the spatially and temporally variable influence of hydrodynamic energy on habitat distribution have been less well studied. Here we investigate the role of wave exposure on patterns of distribution of near-shore benthic habitats. A high resolution spectral wave model was developed for a 624 km2 site along Cape Otway, a major coastal feature of western Victoria, Australia. Comparison of habitat classifications implemented using the Random Forests algorithm established that significantly more accurate estimations of habitat distribution were obtained by including a fine-scale numerical wave model, extended to the seabed using linear wave theory, than by using depth and seafloor morphology information alone. Variable importance measures and map interpretation indicated that the spatial variation in wave-induced bottom orbital velocity was most influential in discriminating habitat classes containing the canopy forming kelp Ecklonia radiata, a foundation kelp species that affects biodiversity and ecological functioning on shallow reefs across temperate Australasia. We demonstrate that hydrodynamic models reflecting key environmental drivers on wave-exposed coastlines are important in accurately defining distributions of benthic habitats. This study highlights the suitability of exposure measures for predictive habitat modeling on wave-exposed coastlines and provides a basis for continuing work relating patterns of biological distribution to remotely-sensed patterns of the physical environment.