In 2008 an initial benthic habitat map was completed by the contractor Avineon, Inc. The National Park Service South Florida / Caribbean Network (SFCN) conducted an accuracy assessment of the map and found the overall habitat identification to be acceptable. However, upon further inspection, the soft-bottom habitat classifications displayed a relatively high level of accuracy, while the hard-bottom habitats were below an acceptable level. With the acquisition of new higher resolution side scan sonar data and 2054 field data points from multiple sources, the 2008 map was revised and improved by utilizing these new data sets to produce the 2010 Dry Tortugas benthic habitat map. The 2010 Dry Tortugas benthic habitat map was developed using 13 mapping classes and 1709 polygons totaling an area of 26,229 hectares. All “Unknown” areas (10,444 hectares) in the 2008 map were identified, the line work for the hard-bottom areas was fine-tuned and a mapping layer was developed showing those areas which have a higher potential for fish and benthic biodiversity. In addition, a final bathymetry layer for the park was developed by merging the existing light detection and ranging (LiDAR) and newly acquired side scan sonar/bathymetry data. The current management plan for the Dry Tortugas National Park (DRTO) marine areas focuses much of its effort on the Research Natural Area (RNA). The intensive amount of research effort placed on the RNA has also accomplished the research needed for the rest of DRTO because current research and monitoring efforts are split equally between areas of the DRTO that fall within and outside the RNA to make for a balanced comparative study design. In February of 2007, National Park Service (NPS) and Florida Fish and Wildlife Conservation Commission (FWC) developed a science plan to assess conservation effectiveness for the RNA in conjunction with the rest of DRTO and the two nearby existing marine reserves. The implementation of the science plan has been accomplished through collaboration and cooperation of federal and state agencies, academic scientists, and NPS. The new benthic habitat map and corresponding products will help in showing what types of marine habitats are located in the Dry Tortugas National Park and provide the ability to track whether management interventions are effectively protecting the environment and associated resources.

Coral reefs are priority habitats which are vulnerable to natural and anthropogenic disturbances. These can cause phase shifts from coral habitat to degraded algal-dominated states – and consequent changes in the distribution, abundance and activity of associated fish species. In the eastern Red Sea, human-induced reef degradation is likely to increase with planned development of the Saudi Arabian coast and the changing climate. The present study therefore investigates the ecological effects of coral-algal phase shifts in reef-associated fish communities, using naturally occurring within-reef benthic zones as proxies for levels of habitat health - with a focus on how these responses differ temporally. These zones were dominated by: hard coral (coral zone), coral and turf algae (transition zone), and macroalgal canopies (algal zone). Six inshore reef areas, were studied in periods with low and high densities of Sargassum in the algal zones (May and November respectively). Community composition was assessed via visual census and predation activity predicted using two proxies: in situ experiments and biomass of carnivores. In both periods, we observed distinct fish communities in each zone - with reduced species richness, Shannon-Wiener diversity and predation intensity, from the coral to the algal zones. Decreases in the abundance and biomass of fish also occurred from the coral to algal zones in May but a spike, as well as a shift in community composition, occurred in the algal zone in November. This shift is attributed to the vast increases in grazer biomass, predominantly Siganus luridus, associated with the November bloom of Sargassum canopies. The present study established, the composition and functioning of Red Sea fish communities is spatially and temporally affected by increased macroalgal dominance. This finding supports the need for herbivorous fish to be made a conservation priority in the management and conservation of reef systems in order to prevent phase shifts to algal dominated states. We conclude that if Red Sea reefs are allowed to shift to alternate states, depending on the density of macroalgal canopies, reefs may support high biomass and abundance of fish but the functioning of the fish community will be altered and the diversity lost.

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.

Remote sensing studies based on satellite and aerial imagery have improved our understanding of the morphology and distribution of several shallow reefs along the Red Sea Arabian coast and of the benthic assemblages associated to them (Bruckner et al., 2011; Bruckner et al., 2012; Rowlands et al., 2016). However, data concerning the deeper benthic assemblages' composition and spatial distribution in the central Red Sea are still missing. Using high-resolution acoustic technology and an underwater remotely operated vehicle (ROV), we aim to map, describe, and classify the reefs found in Thuwal's coastal area, filling the information gap by producing the first benthic habitat map of this area and making progress towards the evaluation of shallow and upper mesophotic benthic resources in the Saudi Arabian Red Sea. High-resolution acoustic data was collected using a multibeam echosounder system, which generated a bathymetric model. Based on this, the seafloor features were classified into 12 morphotypes following a visual assessment. Based on the morphotypes classification, 28 sites were visually selected for ground-truthing data acquisition and characterization of the substrate and benthic assemblages using a remotely operated vehicle equipped with an ultra-short baseline (USBL) positioning system. With the information obtained from the bathymetry data and the ROV video transects, a Top-Down approach in which we analyzed, categorized, and classified the data was used to create Thuwal's reefs benthic habitat map in which 23 different benthic habitat types were identified. This research uncovered previously poorly studied reef morphologies in the Red Sea and their associated benthic assemblages. Moreover, this work will help improve the understanding of the spatial distribution of benthic communities located on Thuwal's reefs, giving a baseline with the potential to provide fundamental information that can be used for mapping, management, conservation, and future research at other Red Sea reef sites in Saudi Arabia.

Using a towed underwater video camera system, benthic habitats were classified along transects in a popular offshore fishing area on the West Florida Shelf (WFS) known as “The Elbow.” Additionally, high resolution multibeam bathymetry and co-registered backscatter data were collected for the entire study area. Using these data, full coverage geologic and biotic habitat maps were developed using both unsupervised and supervised statistical classification methodologies. The unsupervised methodology used was k-means clustering, and the supervised methodology used a random forest algorithm. The two methods produced broadly similar results; however, the supervised methodology outperformed the unsupervised methodology. The results of the supervised classification demonstrated “substantial agreement” (κ>0.6) between observations and predictions for both geologic and biotic habitat, while the results of the unsupervised classification demonstrated “moderate agreement” (κ>0.4) between observations and predictions for both geologic and biotic habitat. Comparisons were made with the previously existing map for this area created by Florida Fish and Wildlife Conservation Commission’s Fish and Wildlife Research Institute (FWC-FWRI). Some features are distinguishable in both maps, but the FWC-FWRI map shows a greater extent of low relief hard bottom features than was predicted in our habitat maps. The areas predicted as low relief hard-bottom by FWC-FWRI often coincide with areas of higher uncertainty in the supervised map of geologic habitat from this study, but even when compared with ground-truth points from the towed video rather than predictions, the low relief hard bottom in FWC-FWRI’s map still corresponds to what was identified as sand in the video 73% of the time. The higher uncertainty might be a result of the presence of mixed habitats, differing morphology of hard-bottom, or the presence of sand intermixed with gravel or debris. More ground-truth samples should be taken in these areas to increase the confidence of these classifications and resolve discrepancies between the two maps. Data from the towed video system were also used to assess differences in fish communities among habitat types and to calculate habitat-specific densities for each taxa. Fish communities were found to significantly differ between soft and hard bottom habitats as well as among the hard-bottom habitats with different vertical relief (flat hard-bottom vs more steeply sloping areas). Additionally, significant differences were found between the fish communities in habitats with attached fauna such as sponges and gorgonians, and areas without attached fauna; however, attached fauna require rock to attach to and the rock habitats rarely lacked attached fauna, so this difference may just reflect the difference between fish communities in sand and rock habitats without the consideration of vertical relief. Moreover, the species driving the differences in the fish communities were identified. Fish were more likely to be present and assemblages were more species rich in more complex habitats (rockier, higher relief, presence of attached fauna). Habitat specific densities were calculated for each species, and general trends are discussed. Lastly the habitat-specific densities were extrapolated to the total area of habitat type (sand vs rock) as predicted by the supervised geologic habitat map. There is predicted to be approximately 111,000 fish (95% CI [67015, 169405]) within the study area based on this method, with ~47,000 (~43%) predicted to be within the sand habitat and ~64,000 (~57%) in the rock habitat. This demonstrates the potential of offshore rocky reefs as “critical habitats” for demersal fish in the offshore environment as rock accounts for just 4% of the study area but is expected to contain over half of the total abundance. The value of sand habitats is also shown, as due to their large area they are able to contribute substantially to the total number of fish despite sustaining comparatively low densities.

Anthropogenic changes to the landscape, storm events and sea level rise are contributing to the erosion of beaches leading to an increase of the sediment load in near shore marine environments. Palm Beach, Florida is host to unique near shore hardbottom habitats. These areas are distinct from the vast expanses of surrounding sediments and play and important role of habitat and shelter for many different species. In this study, remotely sensed images from 2000-2015 were used to look at the movement of sediment and how it contributes to exposure rates of near shore hardbottom habitats in Palm Beach, Florida and how these factors affect the benthic community. GIS was used to determine areas of hardbottom with high exposure (exposed in >60% of aerial images), medium exposure (40-60%), and low exposure ( I strived to determine if one can detect a successional relationship of benthic communities in a dynamic environment with annual mapping. I also examined if areas with higher exposure rates have more complex successive communities than those with lower exposure rates, and what implications this has on near shore benthic communities. In situ surveys conducted at 117 sites determined the community structure (corals, octocorals, macroalgae, and hydroids). This study confirmed that periodic mapping was successful in identifying hardbottom burial and exposure, which fluctuate both spatially and temporally. This periodic mapping along with manual delineation did identify hardbottom burials and exposures that fluctuate between years and relate to benthic community differences. The near shore hardbottom coral reef communities aligned with the observed exposure categories with the greater coral species richness and octocoral morphologies found at sites classified as highly exposed. Statistical analyses showed differences in communities shallower and deeper than three meters’ depth. Increasing the frequency of imagery captures and in situ observation would further increase our comprehension of the metrics of hardbottom exposures in reference to community structure.

The aim of this study was to develop and examine the use of backscatter data collected with multibeam sonar (MBS) systems for benthic habitat mapping. Backscatter data were collected from six sites around the Australian coastal zone using the Reson SeaBat 8125 MBS system operating at 455 kHz. Benthic habitats surveyed in this study included: seagrass meadows, rhodolith beds, coral reef, rock, gravel, sand, muddy sand, and mixtures of those habitats. Methods for processing MBS backscatter data were developed for the Coastal Water Habitat Mapping (CWHM) project by a team from the Centre for Marine Science and Technology (CMST). The CMST algorithm calculates the seafloor backscatter strength derived from the peak and integral (or average) intensity of backscattered signals for each beam. The seafloor backscatter strength estimated from the mean value of the integral backscatter intensity was shown in this study to provide an accurate measurement of the actual backscatter strength of the seafloor and its angular dependence. However, the seafloor backscatter strength derived from the peak intensity was found to be overestimated when the sonar insonification area is significantly smaller than the footprint of receive beams, which occurs primarily at oblique angles. The angular dependence of the mean backscatter strength showed distinct differences between hard rough substrates (such as rock and coral reef), seagrass, coarse sediments and fine sediments. The highest backscatter strength was observed not only for the hard and rough substrate, but also for marine vegetation, such as rhodolith and seagrass. The main difference in acoustic backscatter from the different habitats was the mean level, or angle-average backscatter strength. However, additional information can also be obtained from the slope of the angular dependence of backscatter strength. / It was shown that the distribution of the backscatter. The shape parameter was shown to relate to the ratio of the insonification area (which can be interpreted as an elementary scattering cell) to the footprint size rather than to the angular dependence of backscatter strength. When this ratio is less than 5, the gamma shape parameter is very similar for different habitats and is nearly linearly proportional to the ratio. Above a ratio of 5, the gamma shape parameter is not significantly dependent on the ratio and there is a noticeable difference in this parameter between different seafloor types. A new approach to producing images of backscatter properties, introduced and referred to as the angle cube method, was developed. The angle cube method uses spatial interpolation to construct a three-dimensional array of backscatter data that is a function of X-Y coordinates and the incidence angle. This allows the spatial visualisation of backscatter properties to be free from artefacts of the angular dependence and provides satisfactory estimates of the backscatter characteristics. / Using the angle-average backscatter strength and slope of the angular dependence, derived by the angle cube method, in addition to seafloor terrain parameters, habitat probability and classification maps were produced to show distributions of sand, marine vegetation (e.g. seagrass and rhodolith) and hard substrate (e.g. coral and bedrock) for five different survey areas. Ultimately, this study demonstrated that the combination of high-resolution bathymetry and backscatter strength data, as collected by MBS, is an efficient and cost-effective tool for benthic habitat mapping in costal zones.

Xestospongia muta, the giant barrel sponge, is a key component of coral reef benthic communities in Southeast Florida and the Caribbean. Xestospongia muta increases habitat complexity and stability, and filters large volumes of water, enhancing water quality and facilitating nutrient cycling. Therefore, it is important to investigate trends in the X. muta population on Southeast Florida reefs in response to anthropogenic stressors, changing environmental conditions and acute disturbances and how these events affect its ecological role in the benthic community. This study identified trends in X. muta population density, volume, and size class distribution over time and across reef habitats on the Southeast Florida Reef Tract (SEFRT). Density and volume changes were also investigated following acute physical disturbance caused by Hurricane Irma in September of 2017. Images and demographic data collected at 41 permanent sites from two long-term monitoring projects, The Southeast Florida Coral Reef Evaluation and Monitoring Project (SECREMP) and the Broward County Biological Monitoring Project (BC BIO), were used to evaluate the X. muta population trends. My analysis of the data from 2003 to 2018 shows that Xestospongia muta densities and volume increased over time regionally on the SEFRT and increased on the nearshore, middle, and outer reefs of the SEFRT. Xestospongia muta was found to be more abundant on the SEFRT compared to other locations including the Bahamas, the Florida Keys, Colombia, Belize and Saba. Highest mean density on the SEFRT was 0.35 individuals m-2 ±0.04 SEM, which was higher than the mean densities between 0.21 and 0.29 individuals m-2 at the Caribbean sites previously mentioned. Xestospongia muta individuals were categorized into size classes by volume to investigate density distribution of size classes on the SEFRT. Greater abundances in the smallest of five size classes (≤143.13 cm3) drove the increasing density trends. Despite the increasing trends from 2003 to 2017 with a peak in density and volume in 2017, Hurricane Irma caused a region-wide decline in population density and volume as well as a loss of individuals within the largest size class by volume (>17383.97 cm3). These results indicate that the X. muta population is exhibiting increasing long-term trends on the SEFRT, but also demonstrate that acute physical disturbances have a significant impact on the demographics of the population. Because of this sponge’s multiple roles in the reef communities, these trends have implications for structural complexity, nutrient cycling, water filtration, as well as carbon sequestration on the SEFRT.

Graduation date: 2006 / Structure-forming invertebrates belong to a polyphyletic group of primarily sessile and sedentary megafauna that can significantly enhance the complexity of physical habitats. A number of these organisms, including cold-water corals and sponges, are known to be slow growing and vulnerable to physical disturbance. In addition, as filter feeders, these invertebrates can indicate areas of consistently favorable conditions for feeding and growth. This study provides the first quantitative analysis of structure-forming invertebrate communities in many areas along the continental margin of Oregon and Washington. Geological surveys during 1992-95, using the occupied submersible, Delta, sampled an extensive area in this region, primarily on and around rock outcrops. The videos from these surveys were analyzed to inventory and catalog sessile structure-forming invertebrates and to document their associations with geological habitat types. Detailed data on geological substrate, invertebrate diversity, abundance, and density were compiled and analyzed. It was found that geological substrate and depth were reliable indicators of suitable habitat for most species included in the study. Gorgonian corals tended to concentrate in high densities in depths between 200-250m, at the southern edges of submerged rocky banks, and where hard rocky substrate was covered with a thick layer of sediment. Because of recent fishery regulation changes, this information can be used as baseline data for future studies on the effectiveness of closed areas on the recovery of structure-forming invertebrates from disturbance, particularly bottom trawling.

Intra-archipelago waterways, including tidal strait networks, present a complex set of barriers to, and conduits for sediment transport between marine basins. Tidal straits may also be the least well understood tide-dominated sedimentary environment. To address these issues, currents, sediment transport pathways, and seabed sedimentology & geomorphology were studied in the central Salish Sea (Gulf and San Juan Islands region) of British Columbia, Canada and Washington State, USA. A variety of data types were integrated: 3D & 2D tidal models, multibeam bathymetry & backscatter, seabed video, grab samples, cores and seismic reflection. This dissertation included the first regional sediment transport modelling study of the central Salish Sea. Lagrangian particle dispersal simulations were driven by 2D tidal hydrodynamics (~59-days). It was found that flood-tide dominance through narrow intra-archipelago connecting straits resulted in the transfer of sediment into the inland Strait of Georgia, an apparent sediment sink. The formative/maintenance processes at a variety of seabed landforms, including a banner bank with giant dunes, were explained with modelled tides and sediment transport. Deglacial history and modern lateral sedimentological and morphological transitions were also considered. Based on this modern environment, adjustments to the tidal strait facies model were identified. In addition, erosion and deposition patterns across the banner bank (dune complex) were monitored with 8-repeat multibeam sonar surveys (~10 years). With these data, spatially variable bathymetric change detection techniques were explored: A) a cell-by-cell probabilistic depth uncertainty-based threshold (t-test); and B) coherent clusters of change pixels identified with the local Moran's Ii spatial autocorrelation statistic. Uncertainty about volumetric change is a considerable challenge in seabed change research, compared to terrestrial studies. Consideration of volumetric change confidence intervals tempers interpretations and communicates metadata. Techniques A & B may both be used to restrict volumetric change calculations in area, to exclude low relative bathymetric change signal areas. / Graduate / 2018-12-07