Coral Remote Sensing Workshop: Proceedings and Recommendations, 17-18 September, Sheraton, Brickell Ave, Miami FL

Coral reefs exist in warm, clear, and relatively shallow marine waters worldwide. These complex assemblages of marine organisms are unique, in that they support highly diverse, luxuriant, and essentially self-sustaining ecosystems in otherwise nutrient-poor and unproductive waters. Coral reefs are highly valued for their great beauty and for their contribution to marine productivity. Coral reefs are favorite destinations for recreational diving and snorkeling, as well as commercial and recreational fishing activities. The Florida Keys reef tract draws an estimated 2 million tourists each year, contributing nearly $800 million to the economy. However, these reef systems represent a very delicate ecological balance, and can be easily damaged and degraded by direct or indirect human contact. Indirect impacts from human activity occurs in a number of different forms, including runoff of sediments, nutrients, and other pollutants associated with forest harvesting, agricultural practices, urbanization, coastal construction, and industrial activities. Direct impacts occur through overfishing and other destructive fishing practices, mining of corals, and overuse of many reef areas, including damage from souvenir collection, boat anchoring, and diver contact. In order to protect and manage coral reefs within U.S. territorial waters, the National Oceanic and Atmospheric Administration (NOAA) of the U.S. Department of Commerce has been directed to establish and maintain a system of national marine sanctuaries and reserves, and to monitor the condition of corals and other marine organisms within these areas. To help carry out this mandate the NOAA Coastal Services Center convened a workshop in September, 1996, to identify current and emerging sensor technologies, including satellite, airborne, and underwater systems with potential application for detecting and monitoring corals. For reef systems occurring within depths of 10 meters or less (Figure 1), mapping location and monitoring the condition of corals can be accomplished through use of aerial photography combined with diver surveys. However, corals can exist in depths greater than 90 meters (Figure 2), well below the limits of traditional optical imaging systems such as aerial or surface photography or videography. Although specialized scuba systems can allow diving to these depths, the thousands of square kilometers included within these management areas make diver surveys for deeper coral monitoring impractical. For these reasons, NOAA is investigating satellite and airborne sensor systems, as well as technologies which can facilitate the location, mapping, and monitoring of corals in deeper waters. The following systems were discussed as having potential application for detecting, mapping, and assessing the condition of corals. However, no single system is capable of accomplishing all three of these objectives under all depths and conditions within which corals exist. Systems were evaluated for their capabilities, including advantages and disadvantages, relative to their ability to detect and discriminate corals under a variety of conditions. (PDF contains 55 pages

Hyperspectral benthic mapping from underwater robotic platforms

We live on a planet of vast oceans; 70% of the Earth's surface is covered in water. They are integral to supporting life, providing 99% of the inhabitable space on Earth. Our oceans and the habitats within them are under threat due to a variety of factors. To understand the impacts and possible solutions, the monitoring of marine habitats is critically important. Optical imaging as a method for monitoring can provide a vast array of information however imaging through water is complex. To compensate for the selective attenuation of light in water, this thesis presents a novel light propagation model and illustrates how it can improve optical imaging performance. An in-situ hyperspectral system is designed which comprised of two upward looking spectrometers at different positions in the water column. The downwelling light in the water column is continuously sampled by the system which allows for the generation of a dynamic water model. In addition to the two upward looking spectrometers the in-situ system contains an imaging module which can be used for imaging of the seafloor. It consists of a hyperspectral sensor and a trichromatic stereo camera. New calibration methods are presented for the spatial and spectral co-registration of the two optical sensors. The water model is used to create image data which is invariant to the changing optical properties of the water and changing environmental conditions. In this thesis the in-situ optical system is mounted onboard an Autonomous Underwater Vehicle. Data from the imaging module is also used to classify seafloor materials. The classified seafloor patches are integrated into a high resolution 3D benthic map of the surveyed site. Given the limited imaging resolution of the hyperspectral sensor used in this work, a new method is also presented that uses information from the co-registered colour images to inform a new spectral unmixing method to resolve subpixel materials

Coral Colony-Scale Rugosity Metrics and Applications for Assessing Temporal Trends in the Structural Complexity of Coral Reefs.

Globally, coral reefs are experiencing reductions in structural complexity, primarily due to a loss of key reef building taxa. Monitoring these changes is difficult due to the time-consuming nature of in-situ measurements and lack of data concerning coral genus-specific contributions to reef structure. This research aimed to develop a new technique that uses coral colony level data to quantify reef rugosity (a 3-dimensional measure of reef structure) from three sources of coral survey data: 2D video imagery, line intercept data and UAV imagery. A database of coral colony rugosity data, comparing coral colony planar and contour length for 40 coral genera, 14 morphotypes and 9 abiotic reef substrates, was created using measurements from the Great Barrier Reef and Natural History Museum. Mean genus rugosity was identified as a key trait related to coral life history strategy. Linear regression analyses (y = mx) revealed statistically significant (p < 0.05) relationships between coral colony size and rugosity for every coral genus, morphotype and substrate. The gradient governing these relationships was unique for each coral taxa, ranging from mean = 1.23, for (encrusting) Acanthastrea, to m = 3.84, for (vase-shape) Merulina. These gradients were used as conversion factors to calculate reef rugosity from linear distances measured in video transects of both artificial reefs, used as a control test, and in-situ natural coral reefs, using Kinovea software. This calculated, ‘virtual’ rugosity had a strong, positive relationship with in-situ microscale rugosity (r2 = 0.96) measured from the control transects, but not with that measured at the meso-scale in natural, highly heterogeneous reef environments (r2 < 0.2). This showed that the technique can provide accurate rugosity information when considered at the coral colony level. The conversion factors were also applied to historic line intercept data from the Seychelles, where temporal changes in calculated rugosity were consistent with changes in coral cover between 2008 and 2017. Finally, on application to 2,283 corals digitised from UAV imagery of the Maldives, the conversion factors enabled calculation of rugosity for three 100 m2 reef areas and prediction of how this rugosity will decrease during two future scenarios of coral reef degradation and community change. The study highlights that the application of genera-specific coral rugosity data to both new and existing coral reef survey datasets could be a valuable tool for monitoring reef structural complexity over large spatial scales

Chemical and physical dynamics of marine pockmarks with insights into the organic carbon cycling on the Malin Shelf and in Dunmanus Bay, Ireland.

Pockmarks are specific type of marine geological setting resembling craters or pits. They are considered surface expression of fluid flow in the marine subsurface. Pockmarks are widespread in the aquatic environment but the understanding of their formation mechanisms, relationship with marine macro- and micro-biota and their geochemistry remains limited. Despite numerous findings of these features in Irish waters they received little attention and remain poorly studied. In this work extensive geophysical data sets collected by the Irish National Seabed Survey and its successor the INFOMAR project as well in situ sediment samples were utilized to provide baseline information on the nature of some of these features, the processes they are fuelled by and their geochemical characteristics. Pockmarks from open shelf (Malin Shelf) and bay, fjord like environment (Dunmanus Bay) are compared and theories of their formation are formulated. Sediment from these features was extensively studied utilizing advanced geotechnical and geochemical tools to describe and quantify processes taking place in the subsurface. Organic matter was characterized on a molecular level by combined biomarker and advanced Nuclear Magnetic Resonance approach

Determining potential for pollutant impacts in dynamic coastal waters: comparing morphological settings

The coastal focus and beach culture of Australia’s population in general, and the people of New South Wales in particular, mean that coastal systems are both highly prized and subjected to great pressures. The vast majority of the wastewater generated by the 7.3 million people of New South Wales is discharged directly to the ocean. The dispersion and fate of waterborne pollutants and their potential to impact coastal ecosystems are fundamentally determined by the dynamics of the coastal boundary layer (CBL). This turbulent interface between the coastline and the deep oceans is defined and classified for the first time in this thesis. Coastal morphologies and changes in the orientation of the coastline promote turbulence and strong gradients with extreme variability and heterogeneity over a broad range of scales. Conceptual models are presented to characterise New South Wales coastal boundary layer processes. The broad aims of this thesis are to investigate the coastal boundary layer processes that affect dispersal and advection of pollutants, and to develop conceptual models and tools to facilitate coastal management. Remote sensed ocean colour and sea surface temperature observations define meso-scale CBL phenomena, and this study demonstrates their application to support management decisions in relation to marine algal (phytoplankton) blooms. However, considerable scope exists to improve regional algorithms to deliver better ocean colour products for the optically complex (Case 2) waters of the inner coastal boundary layer. Past failures to consider the CBL (morphological) settings of pollutant discharges to coastal waters have led to inefficient pollutant discharge systems and potential environmental impacts. Two case studies, investigate the principal forcing mechanisms and demonstrate the importance of morphology in controlling the dispersion and retention times of pollutants. The first case study is focused on Sydney coastal waters where pollutant loadings are greater in magnitude and different in character than elsewhere in New South Wales. Here population pressures generate large wastewater loadings but the distances to offshore discharge locations are large compared to the scale of coastal roughness (headlands and bays) and the water is deep, thus reducing the risk of local retention of pollutants and increasing the potential for rapid dilution. By considering simulations of near field effluent plume behaviour in relation to long term ambient nutrient patterns specific periods of the year and depth intervals have been identified when outfalls would have an increased opportunity to influence bloom development, especially the upper half of the water column during late summer. However, algal blooms appear to be principally driven by seasonal oceanic nutrient enrichment. The research presented in this thesis, together with companion research previously published by the author and routine ongoing monitoring, indicate the viability of disposal of the Sydney’s excess sewage effluent (after source control and re-use options have been exhausted) via existing deepwater outfalls. In contrast, inner CBL settings with coastal irregularities (e.g. headlands and bays) have a greater propensity to trap pollutants. A new hydrodynamically relevant morphological classification of New South Wales bays, headlands and islands provides both broad context for case studies and guides preliminary assessments for other locations. This classification reveals a borderline propensity for flow separation and re-circulation in the lee of Corambirra Point which is the focus of the second case study off Coffs Harbour in northern NSW. Direct observations and 3D finite difference hydrodynamic (Eulerian) and particle tracking (Lagrangian) model simulations quantify transient re-circulation associated with local current accelerations and a persistent shear zone located in the wake to the south of Corambirra Point. The flux of ambient water across the prescribed outfall alignment increases eighteen fold, over a shear zone spanning a cross-shore distance of just 1.4km (from 1.6km to 3km offshore). In contrast, the potential for re-entrainment and trapping of effluent in transient re-circulation cells was demonstrated to be insignificant. The proposed location of the outfalls was 1.5km offshore whereas the greatest gain per unit extension of the proposed discharge point coincides with the centre of the shear zone located ~2km offshore. These case studies illustrate specific coastal boundary layer effects and indicate how an understanding of the spatial and temporal scales of these effects can be used to target more specific assessments of potential pollutant impacts. Simple morphological risk assessment tools are also presented to identify factors and processes which limit the exposure of sensitive environments to high pollutant concentrations and loads. Eddy retention effects are generally not incorporated in existing near field models but potential re-entrainment effects in wake zones can be assessed through the eddy retention value, which is introduced in this thesis. Although the approach presented here is focused on New South Wales coastal waters, the framework serves as a basis for general application elsewhere, and as a foundation for further refinement for application to NSW coastal waters. Existing scientific literature indicates that coastal boundary layer processes also shape the distributions of the biological species and communities. This further motivates the development of a process based understanding of coastal boundary layer dynamics as a fundamental platform to support environmental protection and biodiversity conservation initiatives