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The Great Barrier Reef (GBR) is of immense biological, cultural and economic importance, but has also rapidly degraded over the last 30 years. Improved spatial information on reef geomorphic zonation and benthic cover type (including coral type) is critical to support scientific work to understand how the GBR is changing, and to support resource management decisions that enable conservation of the reef and its essential ecosystem services. Yet, no comprehensive maps exist that detail the geomorphic zonation or benthic cover for the GBR’s ~ 3000 reefs. This study presents three new types of shallow reef maps for 237 reefs in the central Cairns Management Region of the GBR Marine Park (GBRMP), explores how the detailed habitat maps created compared to current maps and posits how the new maps may support and refine current critical key science outputs and management challenges. Geomorphic Zonation, Benthic Cover and Coral Type habitat maps were created using a unique combined object-based image analysis and ecological modelling approach that incorporated satellite imagery, limited field data and key reef physical attributes (depth, slope, waves) using a previously peer-reviewed mapping approach developed for the Capricorn Bunker Group reefs, Southern GBR. The mapping approach was consistent and repeatable, suggesting applicability to mapping all 3000 reefs in the GBRMP. Compared to existing maps that only outline each reef, the increase in detail provided by these new habitat maps enabled discrete characterisation of each reef’s geomorphology and benthic composition. With the new habitat maps, areas within each reef can be identified as either coral habitat or not coral habitat. This has not been possible previously. As such, a model of coral ecological and biophysical processes that depends on bottom reflectance of sand and coral areas can be fine-tuned. Similarly, for reef restoration, nursery structures are commonly placed in non-coral habitats, and/or coral larvae are dispersed in areas of known coral habitat. The new habitat maps presented permit more accurate identification of these areas such that restoration projects can be targeted more effectively. These findings confirm the need to now apply this mapping approach to the full extent of the GBR.

Australia’s Great Barrier Reef (GBR) is a globally unique and precious national resource; however, the geomorphic and benthic composition and the extent of coral habitat per reef are greatly understudied. However, this is critical to understand the spatial extent of disturbance impacts and recovery potential. This study characterizes and quantifies coral habitat based on depth, geomorphic and benthic composition maps of more than 2164 shallow offshore GBR reefs. The mapping approach combined a Sentinel-2 satellite surface reflectance image mosaic and derived depth, wave climate, reef slope and field data in a random-forest machine learning and object-based protocol. Area calculations, for the first time, incorporated the 3D characteristic of the reef surface above 20 m. Geomorphic zonation maps (0–20 m) provided a reef extent estimate of 28,261 km2 (a 31% increase to current estimates), while benthic composition maps (0–10 m) estimated that ~10,600 km2 of reef area (~57% of shallow offshore reef area) was covered by hard substrate suitable for coral growth, the first estimate of potential coral habitat based on substrate availability. Our high-resolution maps provide valuable information for future monitoring and ecological modeling studies and constitute key tools for supporting the management, conservation and restoration efforts of the GBR.

The bio-optical properties of coral reef waters were examined across coral reef ecosystems not influenced by land-derived run-off, in the Great Barrier Reef lagoon (Heron Island) and the Coral Sea (the Coringa-Herald and Lihou Reefs). The aim was to determine whether the absorption properties, the concentration-specific absorption properties, and the phytoplankton and non-algal pigmented particle (NAP) absorption concentrations varied from the ocean waters flushing onto the reef at high tide to those waters on the reef or flushing off the reef at low tide. The optical and biogeochemical properties of on-reef waters systematically differed from the surrounding ocean waters. The chl a concentration values varied up to 7-fold and the NAP concentrations up to 29-fold; for the reef samples, the chl a values were on average 2 to 3 times lower than for the oceans whilst the NAP values were slightly higher on the reefs. The spectral absorption values of the chl a, NAP, and colored dissolved organic matter (CDOM) varied up to 6-fold for reef waters and up to 15-fold for ocean waters. The spectral absorption for chl a was up to 3-fold lower on the reef waters, the absorption by the CDOM was up to 2-fold higher and the NAP absorption was 1.6-fold higher on the reef waters. The concentration-specific absorption coefficients for chl a and NAP varied up to 9-fold in reef waters and up to 30-fold in ocean waters. In the case of Heron Island and Coringa-Herald cays, this concentration-specific absorption was on average 1.3 to 1.7-fold higher for chl a and up to 2-fold lower for NAP on the reefs. The Lihou Reef measurements were more ambiguous between the reef waters and ocean waters due to the complex nature and size of this reef. Based on our results, the assumption that the optical properties of on-reef waters and the adjacent ocean waters are the same was shown to be invalid. Ocean waters flowing on to the reef are higher in phytoplankton, whilst waters on the reef or flowing off the reefs are higher in CDOM and NAP. We found differences in the pico,- nano-, and microplankton distributions as well as in the ratios of photosynthetic to photoprotective pigments. The variability in the bio-optical properties between the reef waters and adjacent ocean waters has implications for the estimations of sunlight absorption along the water column, the UV penetration depth, the temperature distributions, and the nutrient and carbon fluxes in coral reef ecosystems. As Earth observation algorithms require proper parameterization for the water column effects when estimating benthic cover, the actual optical properties need to be used. These results will improve the use of Earth observation to systematically map the differences in the water quality between reefs and the adjacent ocean.

There is a requirement for effective, worldwide monitoring of the health of coral reef systems, in particular the coral bleaching phenomenon. The transient nature of bleaching events, the extent and remoteness of tropical reefs, and the complex nature of the light field in submerged coral reef environments, requires novel and sophisticated remote sensing-based detection and monitoring approaches. An objective, physics-based approach (SAMBUCA) was developed for retrieving water column concentrations, bathymetry, and bottom substrate composition from remote sensing data on a per-pixel basis. MERIS images, offering a suitable spatial and temporal coverage for monitoring coral bleaching, were acquired before and during a minor bleaching event at Heron reef (Australia) in 2004. Benthic field surveys, conducted during and after the bleaching event, were analysed, and the optical properties of Heron reef substrates and waters were investigated. The latter represents the most comprehensive optical characterisation of tropical coral waters. SAMBUCA was parameterised with the optical properties of Heron coral reef waters and benthos, and applied to the FR MERIS data. Bathymetry was mapped to a high degree of accuracy, optically deep water was identified, and changes in benthic substrate composition were inferred pointing towards a minor bleaching event. Changes in per-pixel percent cover of live coral were used as a proxy indicator of coral bleaching. This study showed that environmental information on coral bleaching may be objectively retrieved at the appropriate scales for climate change assessment. Further development and validation of applying the SAMBUCA physics-based approach to global remote sensing data is recommended. Ultimately, this may lead to the implementation of regional or global tropical coral health monitoring systems. The approach presented in this thesis is unique in its application of radiative transfer theory to coral reef environments. It is furthermore applicable to other areas such as seagrass beds, and this thesis therefore represents a significant contribution to the remote sensing of (optically shallow) aquatic environments.

[...] other phenomena that cause dampening of capillary waves, such as biological films, hydrodynamic effects, bathymetrie features and even weather-induced artifacts, lead to a range of false-positive interpretations of oil slicks in SAR imagery. [...] SAMSSARA outputs georeferenced maps (shapefiles) of all classified potential targets.

Importantly, physics-based methods-as opposed to empirical methods-require no known information of the study area. [...]they can be applied independent of a satellite sensor (i.e., MODIS, Landsat, RapidEye or Worldview-2) or study area. Throughout the past 20 years, EOMAP and German Aerospace Center (DLR) scientists have developed a unique physics-based modular inversion and processing system (MIP), which includes all the relevant processing steps to guarantee a robust, standardized and operational retrieval of water quality parameters from satellite data.