Benthic and substrate cover data derived from photo-transect surveys in Heron Reef

Underwater georeferenced photo-transect survey was conducted on September 23 - 27, 2007 at different sections of the reef flat, reef crest and reef slope in Heron Reef. For this survey a snorkeler or diver swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. A standard digital compact camera was placed in an underwater housing and fitted with a 16 mm lens which provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey diver/snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry-bag and logged its position as it floated at the surface while being towed by the photographer. A total of 3,586 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned to 1 out of 80 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to gps coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South.

Spectral reflectance library of selected biotic and abiotic coral reef features in Heron Reef

Underwater spectral reflectance was measured for selected biotic and abiotic coral reef features of Heron Reef from June 25-30, 2006. Spectral reflectance's of 105 different benthic types were obtained in-situ. An Ocean Optics USB2000 spectrometer was deployed in an custom made underwater housing with a 0.5 m fiber-optic probe mounted next to an artificial light source. Spectral readings were collected with the probe(bear fibre) about 5 cm from the target to ensure that the target would fill the field of view of the fiber optic (FOV diameter ~4.4 cm), as well as to reduce the attenuating effect of the intermediate water (Roelfsema et al., 2006). Spectral readings included for one target included: 1 reading of the covered spectral fibre to correct for instrument noise, 1 reading of spectralon panel mounted on divers wrist to measure incident ambient light, and 8 readings of the target. Spectral reflectance was calculated for each target by first subtracting the instrument noise reading from each other reading. The corrected target readings were then divided by the corrected spectralon reading resulting in spectral reflectance of each target reading. An average target spectral reflectance was calculated by averaging the eight individual spectral reflectance's of the target. If an individual target spectral reflectance was visual considered an outlier, it was not included in the average spectral reflectance calculation. See Roelfsema at al. (2006) for additional info on the methodology of underwater spectra collection.

Bathymetric map of Heron Reef, Australia, derived from airborne hyperspectral data at 1 m resolution

A simple method for efficient inversion of arbitrary radiative transfer models for image analysis is presented. The method operates by representing the shape of the function that maps model parameters to spectral reflectance by an adaptive look-up tree (ALUT) that evenly distributes the discretization error of tabulated reflectances in spectral space. A post-processing step organizes the data into a binary space partitioning tree that facilitates an efficient inversion search algorithm. In an example shallow water remote sensing application, the method performs faster than an implementation of previously published methodology and has the same accuracy in bathymetric retrievals. The method has no user configuration parameters requiring expert knowledge and minimizes the number of forward model runs required, making it highly suitable for routine operational implementation of image analysis methods. For the research community, straightforward and robust inversion allows research to focus on improving the radiative transfer models themselves without the added complication of devising an inversion strategy.

Benthic cover map of Heron Reef derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Providing accurate maps of coral reefs where the spatial scale and labels of the mapped features correspond to map units appropriate for examining biological and geomorphic structures and processes is a major challenge for remote sensing. The objective of this work is to assess the accuracy and relevance of the process used to derive geomorphic zone and benthic community zone maps for three western Pacific coral reefs produced from multi-scale, object-based image analysis (OBIA) of high-spatial-resolution multi-spectral images, guided by field survey data. Three Quickbird-2 multi-spectral data sets from reefs in Australia, Palau and Fiji and georeferenced field photographs were used in a multi-scale segmentation and object-based image classification to map geomorphic zones and benthic community zones. A per-pixel approach was also tested for mapping benthic community zones. Validation of the maps and comparison to past approaches indicated the multi-scale OBIA process enabled field data, operator field experience and a conceptual hierarchical model of the coral reef environment to be linked to provide output maps at geomorphic zone and benthic community scales on coral reefs. The OBIA mapping accuracies were comparable with previously published work using other methods; however, the classes mapped were matched to a predetermined set of features on the reef.

Airborne hyperspectral image data of Heron Reef, Australia

This airborne hyperspectral (19 bands) image data of Heron Reef, Great Barrier Reef, Australia is derived from Compact Airborne Spectrographic Imager (CASI) data acquired on 1st and 3rd of July 2002, latitude -23.45, longitude 151.92. Processing and correction to at-surface data was completed by Karen Joyce (Joyce, 2004). Raw imagery consisted several images corresponding to the number of flight paths taken to cover the entire Heron Reef. Spatial resolution is one meter. Radiometric corrections converted the at-sensor digital number values to at surface spectral radiance values using sensor specific calibration coefficients and CSIRO's c-WomBat-c atmospheric correction software. Geometric corrections were done using field collected coordinates of features identified in the image. Projection used was Universal Transverse Mercator Zone 56 South and Datum used was WGS 84. Image data is in TIFF format.

Microphytobenthos composition in Heron Reef, Australia, by High Performance Liquid Chromatography (HPLC) (July 2012)

We quantified pigment biomarkers by high performance liquid chromatography (HPLC) to obtain a broad taxonomic classification of microphytobenthos (MPB) (i.e. identification of dominant taxa). Three replicate sediment cores were collected at 0, 50 and 100 m along transects 5-9 in Heron Reef lagoon (n=15) (Fig. 1). Transects 1-4 could not be processed because the means to have the samples analysed by HPLC were not available at the time of field data collection. Cores were stored frozen and scrapes taken from the top of each one and placed in cryovials immersed in dry ice. Samples were sent to the laboratory (CSIRO Marine and Atmospheric Research, Hobart, Australia) where pigments were extracted with 100% acetone during fifteen hours at 4°C after vortex mixing (30 seconds) and sonication (15 minutes). Samples were then centrifuged and filtered prior to the analysis of pigment composition with a Waters - Alliance HPLC system equipped with a photo-diode array detector. Pigments were separated using a Zorbax Eclipse XDB-C8 stainless steel 150 mm x 4.6 mm ID column with 3.5 µm particle size (Agilent Technologies) and a binary gradient system with an elevated column temperature following a modified version of the Van Heukelem and Thomas (2001) method. The separated pigments were detected at 436 nm and identified against standard spectra using Waters Empower software. Standards for HPLC system calibration were obtained from Sigma (USA) and DHI (Denmark).

GPS linked photos of benthic cover transect surveys in Heron Reef

Underwater photo-transect surveys were conducted on September 23-27, 2007 at different sections of the reef flat, reef crest and reef slope in Heron Reef. This survey was done by swimming along pre-defined transect sites and taking a picture of the bottom substrate parallel to the bottom at constant vertical distance (30cm) every two to three metres. A total of 3,586 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of transect surveys. Approximation of the coordinates for each benthic photo was based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software. Coordinates of each photo were interpolated by finding the the gps coordinates that were logged at a set time before and after the photo was captured. The output of this process was an ArcMap point shapefile, a Google Earth KML file and a thumbnail of each benthic photo taken. The data in the ArcMap shapefile and in the Google Earth KML file consisted of the approximated coordinate of each benthic photo taken during the survey. Using the GPS Photo Link extension within the ArcMap environment, opening the ArcMap shapefile will enable thumbnail to be displayed on the associated benthic cover photo whenever hovering with the mouse over a point on the transect. By downloading the GPSPhotoLink software from the www.geospatialexperts.com, and installing it as a trial version the ArcMap exstension will be installed in the ArcMap environment.

Nitrogen ecophysiology of Heron Island, a subtropical coral cay of the Great Barrier Reef, Australia

Coral cays form part of the Australian Great Barrier Reef. Coral cays with high densities of seabirds are areas of extreme nitrogen (N) enrichment with deposition rates of up to 1000 kg N ha(-1) y(-1). The ways in which N sources are utilised by coral cay plants, N is distributed within the cay, and whether or not seabird-derived N moves from cay to surrounding marine environments were investigated. We used N metabolite analysis, N-15 labelling and N-15 natural abundance (delta(15)N) techniques. Deposited guano-derived uric acid is hydrolysed to ammonium (NH4+) and gaseous ammonia (NH3). Ammonium undergoes nitrification, and nitrate (NO3-) and NH4+ were the main forms of soluble N in the soil. Plants from seabird rookeries have a high capacity to take up and assimilate NH4+, are able to metabolise uric acid, but have low rates of NO3- uptake and assimilation. We concluded that NH4+ is the principal source of N for plants growing at seabird rookeries, and that the presence of NH4+ in soil and gaseous NH3 in the atmosphere inhibits assimilation of NO3-, although NO3- is taken up and stored. Seabird guano, Pisonia forest soil and vegetation were similarly enriched in N-15 suggesting that the isotopic enrichment of guano (delta(15)N 9.9parts per thousand) carries through the forest ecosystem. Soil and plants from woodland and beach environments had lower delta(15)N (average 6.5parts per thousand) indicating a lower contribution of bird-derived N to the N nutrition of plants at these sites. The aquifer under the cay receives seabird-derived N leached from the cay and has high concentrations of N-15-enriched NO3- (delta(15)N 7.9parts per thousand). Macroalgae from reefs with and without seabirds had similar delta(15)N values of 2.0-3.9parts per thousand suggesting that reef macroalgae do not utilise N-15-enriched seabird-derived N as a main source of N. At a site beyond the Heron Reef Crest, macroalgae had elevated delta(15)N of 5.2parts per thousand, possibly indicating that there are locations where macroalgae access isotopically enriched aquifer-derived N. Nitrogen relations of Heron Island vegetation are compared with other reef islands and a conceptual model is presented.

Major cellular and physiological impacts of ocean acidification on a reef building coral

As atmospheric levels of CO2 increase, reef-building corals are under greater stress from both increased sea surface temperatures and declining sea water pH. To date, most studies have focused on either coral bleaching due to warming oceans or declining calcification due to decreasing oceanic carbonate ion concentrations. Here, through the use of physiology measurements and cDNA microarrays, we show that changes in pH and ocean chemistry consistent with two scenarios put forward by the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, before affects on biomineralisation are apparent at the phenotype level. Under high CO2 conditions corals at the phenotype level lost over half their Symbiodinium populations, and had a decrease in both photosynthesis and respiration. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrate upregulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur before impacts on calcification.

Wave-generated flow on coral reefs - an analysis for two-dimensional horizontal reef-tops with steep faces

Waves breaking on the seaward rim of a coral reef generate a flow of water from the exposed side of the reef to the sheltered side and/or to either channels through the reef-rim or lower sections of the latter. This wave-generated flow is driven by the water surface gradient resulting from the wave set-up created by the breaking waves. This paper reviews previous approaches to modelling wave-generated flows across coral reefs and discusses the influence of reef morphology and roughness upon these flows. Laboratory measurements upon a two-dimensional horizontal reef platform with a steep reef face provide the basis for extending a previous theoretical analysis for wave set-up on a reef in the absence of a flow [Gourlay, M.R., 1996b. Wave set-up on coral reefs. 2. Set-up on reefs with various profiles. Coastal Engineering 28, 1755] to include the interaction between a unidirectional flow and the wave set-up. The laboratory model results are then used to demonstrate that there are two basic reef-top flow regimes-reef-top control and reef-rim control. Using open channel flow theory, analytical relationships are derived for the reef-top current velocity in terms of the offreef wave conditions, the reef-top water depth and the physical characteristics of the reef-top topography. The wave set-up and wave-generated flow relationships are found to predict experimental values with reasonable accuracy in most cases. The analytical relationships are used to investigate wave-generated flows into a boat harbour channel on Heron Reef in the southern Great Barrier Reef. (c) 2005 Elsevier B.V. All rights reserved.

Spatial patterns of aerobic and anaerobic mineralization rates and oxygen penetration dynamics in coral reef sediments

Oxygen consumption rates (OCR), aerobic mineralization and sulfate reduction rates (SRR) were studied in the permeable carbonate reef sediments of Heron Reef, Australia. We selected 4 stations with different hydrodynamic regimes for this study. In situ oxygen penetration into the sediments was measured with an autonomous microsensor profiler. Areal OCR were quantified from the measured oxygen penetration depth and volumetric OCR. Oxygen penetration and dynamics (median penetration depths at the 4 stations ranged between 0.3 and 2.2 cm), OCR (median 57 to 196 mmol C m(-2) d(-1)), aerobic mineralization (median 24 to 176 mmol C m(-2) d(-1)) and SRR (median 9 to 42 mmol C m(-2) d(-1)) were highly variable between sites. The supply of oxygen by pore water advection was a major cause for high mineralization rates by stimulating aerobic mineralization at all sites. However, estimated bottom water filtration rates could not explain the differences in volumetric OCR and SRR between the 4 stations. This suggests that local mineralization rates are additionally controlled by factors other than current driven pore water advection, e.g. by the distribution of the benthic fauna or by local differences in labile organic carbon supply from sources such as benthic photosynthesis. Carbon mineralization rates were among the highest reported for coral reef sediments, stressing the role of these sediments in the functioning of the reef ecosystem.

Inhibition of settlement and metamorphosis of the ascidian Herdmania curvata by non-geniculate coralline algae

The surfaces of non-geniculate coralline algae (NCA) are known to induce the settlement and metamorphosis of disparate marine taxa. In this study we investigate the responsiveness of larvae of Herdmania curvata (Ascidiacea: Stolidobranchia) to three species of NCA (Neo-goniolithon brassica-florida, Hydrolithon onkodes, and Lithothamnium prolifer) that cohabit the slope and crest of Heron Reef, Great Barrier Reef. H. curvata larvae were first exposed to these NCA at or within 2 h of hatching, which is 1 to 2 h prior to attaining competence, and then cultured continuously with the NCA for 12 to 14 h. Rates of settlement and metamorphosis of H, curvata cultured in laboratory chambers in the presence of the different NCA were significantly lower than spontaneous rates in seawater. The limited settlement in treatments containing NCA were confined entirely to the chamber periphery, and settlement never occurred on the surface of the NCA. The inhibitory effect was dose-dependent and was stronger in H. brassica-florida and H. onkodes than in L. prolifer. Larvae that did not settle in treatments with NCA had rounded anterior trunks and, in extreme cases, kinked tails with rounded and dissociated tail muscle cells. In some individuals, we observed the anterior chemosensory papillae being sloughed off the larval body. Morphological analysis of trunk ectodermal and mesenchymal nuclei of larvae cultured in the presence of the NCA revealed that general necrotic cell death was occurring. Importantly, H. curvata larvae that were exposed to NCA could not subsequently be induced to metamorphose in KCl-elevated seawater, whereas larvae not exposed to NCA metamorphosed at high rates in KCl-elevated seawater.

Synchronous oogenesis during the semilunar spawning cycle of the tropical abalone Haliotis asinina

On the southern Great Barrier Reef, Haliotis asinina (Vetigastropoda: Pleurotomarioidea) synchronously spawn every 2 wk in a predictable fashion. allowing detailed analysis of reproduction, gametogenesis, and gonad development. Histological examination of the ovaries of members of the Heron Reef population during this semilunar cycle reveals that oogenesis is also synchronous and predictable, and requires more than two spawning cycles (i.e. >28 days) to complete. Shortly after a spawning event the ovary comprises two cohorts of primary oocytes, one of which will be released at the next spawning event, and clusters of oogonia. At this time there is a rapid proliferation and expansion of trabeculae, germinal epithelial, and oogonia, and a dramatic increase in the size of the vitellogenic oocytes to be: spawned at the next spawning event. Within 4 days these oocytes have filled the ovary. On the day of the next spawning a lumen forms in the ovary as a result of localized degradation of trabeculae. The large primary oocytes dissociate from the receding trabeculae. initiate maturation, and accumulate in the lumen; these oocytes become embedded in a jelly coat layer. The next cohort of oocytes remain attached to the trabeculae. The jelly coat appears to be completely dissolved within 30 min of spawning. Comparison of the oogenesis and ovary development in II. asinina with other abalone species indicates that these processes are very similar in tropical and temperate abalone. This suggests that insights into the regulation of reproduction and spawning in H. asinina are likely to be applicable to other haliotids.