Scleractinian corals were recorded from the fringing reefs offshore from the Daintree National Park during a three day study in November 1985. The field study was supplemented by examination of coral specimens collected by other researchers from these reefs. The checklist produced also includes an assessment of the abundance of each coral species. The aim of this study was to produce an inventory of the scleractinian corals on reefs in the Daintree region of north Queensland.

Stratification and flushing of a small lagoon in the windward reef flat of Davies Reef in the central Great Barrier Reef was examined in 1980/1981 using three complementary experiments.In the first experiment, salinity-temperature-depth (STD) profiles were taken each 0.5 hr for 2 days (25-27th April, 1980). On the 27th April at low tide (1400hrs), the resident bottom water of the lagoon was marked with fluorescein dye. The dye was sampled with Niskin bottles, at 2m intervals from and including the bottom every 4 hours until the dye could not be detected. STD profiles were taken concurrently. Dye sampling commenced at 1630hrs, to avoid photodegradation, and fluorescence was measured on an Amico-Bowman spectrophotofluorometer. STD and dye experiments were repeated from the 2-5th November, 1980. Rhodomine dye was used on this occasion to allow daylight sampling and dye profiles were taken at 30 minute intervals. In the second experiment, 7 Aanderaa RCM4 current meters were deployed from the 15th June to 15th July 1980, in a vertical string, with a spacing of 2.7m in a position where the water depth was 20m below the reef flat. Temperature, pressure and vector-current profiles were recorded every 10 minutes. This array functioned as a thermistor string, as currents in the lagoon were near the determination limit of the current meters. An additional Aanderaa RCM4 current meter, measuring currents and water temperature was deployed midway between two lagoons, south west of the study site. Wind vectors were accessed from twice daily recordings at the weather station at the Cape Cleveland lighthouse. In the third experiment temperatures at the top and bottom waters of the lagoon were recorded every 10 minutes between the 24th April 1980 and 21st March 1981. Wind measurements were taken from the weather station at the Cape Cleveland lighthouse. Experiments were undertaken to gain an understanding of thermal stratification and the trapping of bottom water in reef lagoons on three time scales by: 1. using temperature and dyes to mark diurnal events2. studying currents on the reef flat and stratification in the lagoon for 1 month3. using temperature to infer events from a time series of approximately 1 year

Six instruments were deployed on the Scott Cay West Transect (J). Instruments were deployed along a transect down the reef slope.Code: SCW5; Depth: -2.0m; Instrument: Odyssey; Serial #: 6568; Code: SCW4; Depth: -1.0m; Instrument: Odyssey; Serial #: 6538;Code: SCW3; Depth: 1.8m; Instrument: Odyssey; Serial #: 6332;Code: SCW2; Depth: 4.8m; Instrument: Tidbit; Serial #: SL3-31060;Code: SCW1; Depth: 19.8m; Instrument: S4; Serial #: 615; File Name: SCWuvCode: SCW1; Depth: 19.8m; Instrument: SBE16; Serial #: 2123; File Name: SCWct This deployment was a component of the "Physical Environment" sub-project of the project "Biological and Physical Environment at Scott Reef 2003" Two of the temperature loggers were exposed at low tide.

Time series data are often observed in ecological monitoring. Frequently such data exhibit nonlinear trends over time potentially due to complex relationships between observed and auxiliary variables, and there may also be sudden declines over time due to major disturbances. This poses substantial challenges for modelling such data and also for model-based adaptive monitoring. We propose novel methods for finding adaptive designs for monitoring when historical data show such nonlinear patterns and sudden declines over time. This work is motivated by a coral reef monitoring program that has been established at Scott Reef; a coral reef off the Western coast of Australia. Data collected for monitoring the health of Scott Reef are considered, and semiparametric and interrupted time series modelling approaches are adopted to describe how these data vary over time. New methods are then proposed that enable adaptive monitoring designs to be found based on such modelling approaches. These methods are then applied to find future monitoring designs at Scott Reef and form a set of recommendations for future monitoring. Through applying the proposed methods, it was found that future in formation gain is expected to be similar across a variety of different sites, suggesting that no particular location needed to be prioritised at Scott Reef for the next monitoring phase. In addition, it was found that omitting some sampling sites/reef locations was possible without substantial loss in expected information gain, depending upon the disturbances that were observed. The resulting adaptive designs are used to provide recommendations for future monitoring in this region, and for reefs where changes to the current monitoring practices are being sought. Furthermore, as the methods used and developed throughout this study are generic in nature, this research has the potential to improve ecological monitoring more broadly where complex 28 data are being collected over time.

The study consisted of laboratory and field components. Under laboratory conditions, the temperature of standardized individual color chart fields submerged in seawater was determined at contrasting levels of flow and irradiance using a calibrated micro-thermistor with a 1 mm measurement tip. The same method was then used to measure the microtemperature environment around 3 corals (2 massive and 1 branching species) that varied in colony pigmentation from light to dark brown. Coral surface warming at high irradiance (noon) and low irradiance (early morning or late afternoon) in outdoor flow chambers: colonies of the hemispherical species Favia matthai at flow speeds of 1, 2, and 5 cm s-1, and colonies of the digitate species Acropora millepora at flow speeds of 2 and 5 cm s-1. Pigmentation was measured as background fluorescence (F0), determined with pulse-amplitude-modulated fluorometry. The ambient water temperature was 29.38C. In the field, the natural distributions of coral darkness were quantified on 4 reefs across the continental shelf of the Great Barrier Reef, spanning from turbid coastal conditions to clear-water offshore. Reefs were: High Island (a turbid inshore reef with high water nutrient concentrations); Fitzroy Island (an inshore reef with greater water clarity and less exposure to terrestrial runoff from river flood plumes than High Island); Hastings Reef (a mid-to outer-shelf reef, 71% relative distance across the continental shelf); Flynn Reef (on the outermost edge of the continental shelf). Tissue darkness was measured in the first 40 scleractinian coral colonies that were encountered along 6 line intercept transects that ran slope parallel at the windward and leeward side at 4, 8, and 12 m depths (a total of 240 colonies on each reef), including all hard coral species. Measurements of the temperature microenvironment around cnidarians with contrasting darkness on inshore reefs were conducted for 4 consecutive days in January 2005, when sea surface temperatures were 28-29°C, and no signs of coral blanching or bleaching were observed. To assess the effects and interactions of 3 of the factors involved in controlling the temperature microenvironment of coral colony surfaces, namely irradiance, flow, and colony darkness. True measures of short-wave radiation, absorptivity, and convection were not attempted: photosynthetically active irradiance was measured as a proxy for short-wave radiation; colony darkness (pigmentation) was used as a proxy for absorptivity; and water flow was manipulated to vary heat convection from the colony surfaces. The use of these variables helped relate the experimental results to underwater measurements that are readily available in the field.Mean visibility across the continental shelf was estimated by spatial models as 5 m at High Island, 8 m at Fitzroy Island, 18 m at Hastings Reef, and 25 m at Flynn Reef. Concentrations of suspended solids and chlorophyll decreased across these reefs.Cnidarians measured on the reef: the flat-encrusting stony coral Montipora tuberculosa, 4 other species of stony corals (including hemispherical, foliose and branching growth forms), two species of octocorals, and the zoanthid Palythoa. Additionally, surface warming was determined in the dark, thick, sediment trapping turf algal mats on these reefs. The experimental tanks measured Favia matthai, Acropora millepora ,and Porites.A standardized coral color chart printed on a thin, lightly textured plastic sheet was used - 'Coral Health Chart', University of Queensland, Australia: www.CoralWatch.org - the 6 color fields on the chart increase on a log scale from score 1=near-white, to score 6=dark brown.

Fresh leaves of seven species of tropical seagrasses, collected from Magnetic Island, north Queensland, were analysed for sterol and fatty acid composition. The species examined were Cymodocea serrulata, Enhalus acoroides, Halodule uninervis, Halophila ovalis, Halophila ovata, Halophila spinulosa and Thalassia hemprichii.Samples were extracted with CHC13-MeOH (1:1). Sterols and fatty acid methyl esters were prepared from the extracts. Sterols (as the methyl ethers) and fatty acid methyl esters were analysed by GLC.Fatty acids and sterols were identified by their mass spectra and by co-chromatography with standards where available. This research was undertaken to determine if chemical markers were present in seagrass leaves, which would allow seagrass derived material to be traced through coastal ecosystems. Variations in sterol and fatty acid composition were examined for potential chemotaxonomic significance.

Specimens of the decapod shrimp, Acetes sibogae australis, were collected along the jetty of the Australian Institute of Marine Science (AIMS) and specimens of the copepod, Acartia australis, were collected from Davies Reef lagoon. The copepods were transported in a 20 litre bucket to the AIMS laboratory within six hours. In the laboratory each species was transferred to gently aerated aquaria containing unfiltered sea water collected from the same site as the animals and placed in a constant temperature room (24-25°C).Physiological activities and biochemical components were measured for subsamples of Acetes sibogae australis at 2, 14, 26 and 50 hours after capture. Measurements for subsamples of Acartia australis were made at 6, 14, 26 and 49 hours after capture. Respiration and excretion of ammonia and phosphate were measured using a water bottle method. Twelve replicate bottles containing Acetes sibogae australis were incubated for 2.5-3.5 hours, while 8 replicates bottles containing Acartia australis were incubated for 3.5-4.5 hours. At the end of incubation, separate water samples were siphoned off dissolved oxygen analysis and for ammonia and phosphate analyses.Animals from the incubation bottles were filtered onto GF/C filters and frozen in liquid nitrogen and stored in a freezer until analysed within 24 hours. Half of the filters from each experiment were homogenized in trichloroacetic acid for extraction of adenine nucleotides. ATP was determined by the luciferase-luminescence method, and ADP and AMP by the same method after enzymatic conversion to ATP. The remaining GF/C filters were homogenized in ETS-B solution, and these extracts were used to determine electron transport system (ETS) activity and the concentrations of protein and RNA. Laboratory studies were undertaken to investigate the decline in physiological activities, including respiration and excretion rates, of two species of marine zooplankton after capture. The results were used to assess whether capture stress or shortage of food contributed to declines. These experiments were a component of the project "The effect of laboratory conditions on the extrapolation of experimental measurements to the ecology of marine zooplankton".

From January to March 1994, vector-averaging Aanderaa and InterOcean S4 current meters were deployed at four locations along a cross-shelf transect between Bowden Reef and Darley Reef and a fifth current meter was deployed in a gully through the reef crest at Darley Reef. A tide gauge was also deployed in shallow waters at Old Reef. CTD data were collected at each mooring on deployment and on recovery. All current meters and the tide gauge recorded 30 minute averaged data.A series of models were used to calculate currents, predict the trajectories of water born-tracers and calculate tidally-predicted currents. Results from the field and the model were visualised using IBM's Data Explorer. This research was initiated to collect field data to enable modelling of the circulation of water around reefs in a region of high reef density.

Samples of Phyllosoma were collected from trawls conducted on the Great Barrier Reef at depths of 1-100 m in May 2005. Phyllosoma were identified to genus (and to species level when possible) immediately upon collection using a dichotomous key.The total bacterial DNA associated with phyllosoma was extracted from two separately homogenized P. ornatus phyllosoma and one homogenized Panulirus penicillatus phyllosoma using the Qiagen DNeasy Tissue Kit (Qiagen, Hilden, Germany). Bacterial 16S rRNA gene was amplified from DNA extracted from phyllosoma using the primers 27f and 1492r.Partial and complete 16S rRNA gene sequences of bacterial clones were obtained using the primers 27f, 339f, 732f and 1492r; bacterial representatives were found from the following: a-Proteobacteria, Firmicutes, y-Proteobacteria, e-Proteobacteria, Bacteroidetes. Various indices and models were used to analyse the variation of microbial diversity within clone libraries. The genus affiliation of dominant bacterial sequences (Sulfitobacter, uncultured e-proteobacterium, Erythrobacter, Roseobacter, Exiguobacterium, Psychrobacter, Clostridium, Pseudomonas, Alteromonas, Paracoccus) retrieved from the clone libraries was recorded for wild Panulirus ornatus (PO1 and PO2) and Panulirus penicillatus (PP) phyllosoma samples.Phyllosoma samples were analysed by histology (examined using light microscopy to determine any internal lesions or disease); scanning electron microscopy (SEM) to determine bacterial colonization (external or internal); and fluorescence in situ hybridization (FISH) to examine bacteria in tissue sections (without detectable bacterial cells, with low bacterial density, occasional cell accumulations).The GenBank accession numbers assigned for nucleotide sequence data of all phyllosoma clones submitted are:DQ985883, DQ985884, DQ985885, DQ985886, DQ985887, DQ985888, DQ985889, DQ985890, DQ985891, DQ985892, DQ985893, DQ985894, DQ985895, DQ985896, DQ985897, DQ985898, DQ985899, DQ985900, DQ985901, DQ985902, DQ985903, DQ985904, DQ985905, DQ985906, DQ985907, DQ985908, DQ985909, DQ985910, DQ985911, DQ985912, DQ985913, DQ985914, DQ985915, DQ985916, DQ985917, DQ985918, DQ985919, DQ985920, DQ985921, DQ985922, DQ985923, DQ985924, DQ985925, DQ985926, DQ985927, DQ985928, DQ985929, DQ985930, DQ985931, DQ985932, DQ985933, DQ985934, DQ985935, DQ985936, DQ985937. To determine the bacterial community associated with wild-caught, mid-stage larvae of spiny lobsters (Palinuridae) in their native oligotrophic marine environment, and to compare their diversity and composition with communities associated with aquaculture-reared larvae of the tropical rock lobster Panulirus ornatus, the current identified candidate for aquaculture in Australia. The phylogenetic tree included closest relativeves (and accession numbers): Acidovorax sp. (AJ534865), Alteromonas sp. (AF427478), Citromicrobium bathoceanense (Y16267), Clostridium quinii (X76745), Cytophaga marinoflava (M58770), Erythrobacter citreus (AF118020), Exiguobacterium sp. (AY205564), hodothermus marinus (X77140), Pseudoalteromonas sp. (AF239705), Pseudoalteromonas sp. (AJ704790), Pseudoalteromonas sp. (AY258115), Pseudoalteromonas sp. (U80834), Pseudomonas saccharophila (AF368755), Psychrobacter arenosus (AJ609273), Psychrobacter marincola (AJ309941), Psychrobacter pacificensis (AB016054), Psychrobacter pacificensis (AB016055), Psychrobacter sp. (AJ551125), Roseobacter sp. (AJ536669), Staphylococcus saccharolyticus (L37602), uncultured a-Proteobacterium (AY033306), Uncultured e-Proteobacterium (AF367487), Vibrio alginolyticus (AF513447).

The herbivorous copepods, Calanus plumchrus and Paracalanus parvus, the herbivorous euphausiid, Euphausia pacifica, the carnivorous amphipod, Parathemisto pacifica and the carnivorous ctenophore, Pleurobrachia pileus used in this experiment were collected from Saanich Inlet, British Columbia, Canada, between May and August 1975.All animals, except for Paracalanus parvus, which were used immediately, were left overnight in unfiltered sea water collected from the same site as the zooplankton. Zooplankton were then maintained in 300 to 500 ml beakers containing well aerated filtered seawater in a constant temperature room at 10°C ± 1°C. Two different feeding regimes were used for the experiment, with one group of each species fed excess food and the other starved by placing the zooplankton in filtered sea water only. Calanus plumchrus, Paracalanus parvus and Euphausia pacifica were fed a diet of cultured Chaetoceros spp., originally collected from the same site as the zooplankton. Parathemisto pacifica were fed chopped fresh Euphausia pacifica and Pleurobrachia pileus were fed freshly collected Calanus plumchrus.Prior to starting the experiment, a subsample was taken from each species, except for the ctenophore, Pleurobrachia pileus, to establish the mean dry body weight of the experimental animals. At the end of the experiment, the mean dry body weight of the survivors was also determined. Dry body weight was measured by placing specimens in a desiccator over silica-gel at approximately 20°C for 1 week. For Pleurobrachia pileus, the equatorial diameter, measured by placing each specimen with a small amount of sea water in a shallow dish under the dissecting microscope was used as a measure of body size.Respiration rate was measured with an oxygen electrode (YSI oxygen monitor system). Zooplankton were incubated in a 6.3 ml cell with filtered water for 20 to 30 minutes. Rates of ammonia and inorganic phosphate excretion were measured after removing the zooplankters from the cell, rinsing with filtered sea water and incubating in 30 to 40 ml of filtered sea water in a small beaker fitted with a glass lid for 2 to 4 hours. Ammonia and inorganic phosphate were determined by the phenol-hypochlorite and molybdate methods, respectively. Zooplankters, except for Paracalanus parvus, which was too small to handle repeatedly without damage, were then returned to beakers, with or without food, for subsequent measurements. Depending on the species, zooplankters were maintained between 3 and 49 days, with between 3 and 10 respiration and excretion measurements taken over the maintenance period.On day 34 of the experiment, the body surface of starved Calanus plumchrus specimens were observed to be covered with epiphytic pennate diatoms, which were later identified as Navicula spp. Licmophora sp and Synedra sp.. By day 49 both starved and fed Calanus plumchrus were covered with these diatoms. Respiration rates and ammonia and phosphate excretion rates were measured in herbivorous and carnivorous species of zooplankton, maintained under different feeding regimes, to determine whether the previously observed progressive decreases in respiration and excretion rates of some zooplankton species kept in the laboratory after capture, was due food shortage. This experiment is a component of the project "The effect of laboratory conditions on the extrapolation of experimental measurements to the ecology of marine zooplankton".