Three Aanderaa RCM current meters and a S4 current meter were attached to mooring CM1, located north west of John Brewer Reef and in the free stream. The mooring was deployed in 42m of water and the four current meters were attached to the mooring to study changes in current velocity with depth.Deployment Details:Date Deployed: 31/3/1987Date Recovered: 25/8/1987Instruments Deployed:S4 #s620; Depth: 10mRCM #5239; Depth: 18mRCM #4326; Depth: 26mRCM #5278; Depth: 35m The aim of this project was to collect field data to calibrate a numerical model for the combined tidal and wind-forced circulation at John Brewer Reef, and to apply those circulation patterns to calculate the trajectories, residence times and likelihood of outbreaks of crown-of-thorns starfish on areas of the reef. The model boundary was defined by CM1, CM2, CM3, CM4, CM5 and CM13. However, the current meters attached to moorings CM5 (deployed 2/4/87) and CM13 (deployed 1/4/87) were not recovered. Mooring CM4 (deployed 2/4/87)drifted to the Whitsunday Islands. The current meter was badly fouled and the data were unusable.

This research was undertaken to provide quantitative data on the proportions of Acanthaster planci feeding during the day and night. Coral Reef - Condition, Crown of Thorns Starfish - Activity, Crown of Thorns Starfish - Condition, Crown of Thorns Starfish - Diameter, Crown of Thorns Starfish - Outbreak Status, Food - Preference, Lifeform - Benthic, Percentage Cover, Relative Frequency, Substrate Type, Density - Population, Genus, Species These data were used in Chapter 2 of the PHD Thesis, Keesing JK (1990) Feeding biology of the crown-of-thorns starfish, Acanthaster planci (Linnaeus). Ph.D Thesis, James Cook University of North Queensland, Townsville, 197 pp.

Plasma tissue and haemolymph samples from 118 species across a range of phyla were assayed for the presence of saxiphilin [3H]STX, a soluble protein which binds the neurotoxin saxitoxin. Samples of individuals per species ranged from 1 to 18 and phyla were sourced from around the world.Effective concentrations of [3H]STX binding sites (pmol ml-¹) in plasma and tissue samples and (pmol mg-¹) are given for the species which exhibited activity, as well as the material tested (plasma, tissue, haemolypmph) and, in some cases, the geographical source. To survey a range of phyla for the presence of saxiphilin-like activity. The results suggest that the saxiphilin gene is as old as an ancestral gene encoding bilobed transferrin, identified in several arthropods and all the vertebrates in the study.Species (28) found to exhibit saxiphilin-like activity:Teleost fish: Anguilla rostrata (eel); Apogon sp. (cardinal fish); Danio rerio (zebra fish); Gambusia affinis (mosquito fish); Hypostomus plecostomus (catfish); Poecilia reticulata (guppy); Pomacentrus sp. (damsel fish)Lungfish: Protopterus aethopicusAmphibians: Ambystoma tigrinum (tiger salamander); Bufo marinus (cane toad); Notopthalamus viridescens (eastern newt); Rana sylvatica (wood frog); Rana temporaria (grass frog)Reptiles: Varanus rosenbergii (goanna monitor lizard); Sceloporus poinsetti (crevice spiny lizard); Naja naja kaouthia (Thailand cobra); Croalus viridus viridus (rattlesnake); Thamnophis ordinoides and T. sirtalis (garter snakes)Arthropods: Daphnia sp. (water flea); Oniscus sp. (sowbug); Ethmostigmus rubripes (centipede); Araneus cf cavaticus (orb web spider); Actaeodes tomentosus, Chlorodiella nigra, Liomera tristis and Lophozozymus pictor (xanthid crabs).Species (102) which did not contain a detectable amount of saxiphilin binding activity:Acanthaster planci (crown-of-thorns starfish); Acheta domestica (cricket); Acmaea cf testudinalis (limpet); Actinia australis (sea anemone); Alligator mississippiensis (alligator, North America); Anas sp. (duck); Anser anser (domestic goose); Aplysia californica (sea hare); Arothon manilensis (puffer fish); Artemia salina (brine shrimp); Asterius forbesii (starfish); Asterius vulgaris (starfish); Balaenoptera acutorostrata (minke whale); Balberus sp. (cockroach); Bos taurus (cow); Callianassa australiensis (marine yabby); Camponotus pennsylvanicus (carpenter ant); Cancer borealis (Jonah crab); Caretta caretta (loggerhead turtle); Cicada sp. (cicada); Columba lives (domestic pigeon); Crocodylus porosus (crocodile, Australia); Cucumaria frondosa (sea cucumber); Cyclopterus lumpus (lumpfish); Delphinus delphis (common dolphin); Dermestes sp. (dermestid beetle); Dermochelys coriacea (leatherback turtle); Diademnum molli (ascidian); Donax deltoides (bivalve); Drosophila melanogaster (fruit fly); Echinarachnius parma (sand dollar); Eisenia fetida (tiger worm); Elseya dentata (snapping tortoise, Australia); Equus caballus (horse); Eudrilus eugenia (nightcrawler); Gallus gallus (chicken); Gastrolepida calvigea (annelid); Ginglymostoma cirratum (nurse shark); Globicephala malaena (pilot whale); Hippodamia convergens (lady beetle); Holothuria atra (holothurian); Homarus americanus (lobster); Homo sapiens (human); Hyalophora cecropia (silkmoth); Jasps stellifera (sponge); Lagenorhynchus acutus (white-sided dolphin); Lanthella basta (sponge); Latimeria chalumnae (coelacanth); Limulus polyphemus (horseshoe crab); Linckia laevigata (starfish); Lingula sp. (brachiopod); Littorina litorea (periwinkle); Makaira indica (marlin); Manduca sexta (tobacco hornworm moth); Meleagris gallopavo (common turkey); Mordacia mordax (lamprey); Mytilus edulis (bivalve mollusc); Mytilus edulis (blue mussel); Negaprion brevirostrio (lemon shark); Notechis scutatus (Australian tiger snake); Ocypode corimana (ghost crab); Oecophylla smaragdine (green ant); Oncopeltus fasciatus (milkweed bug); Oryctolagus sp. (rabbit); Ovis aries (domestic sheep); Pagurus sp. (hermit crab); Papilio polyxenes (black swallowtail butterfly); Penaeus monodon (tiger prawn); Pericherax heteroraphis (sponge); Periplenata australiensis (cockroach); Polycarpa aurata (ascidian); Polycarpa sp. (ascidian); Pseudemys scripta (red ear turtle, North America); Pseudoceros sp. (flatworm); Pseudopleuronectes americanus (flounder); Raja erinacea (little skate); Rattus norvegicus (rat); Reteterebella queenslandia (polychaete); Reticulitermes flavipes (termite); Rhopoloides odorabile (sponge); Sarcophyton elegans; Saxidomus giganteus (butter clam); Saxidomus giganticus (bivalve mollusc); Scomber scombrus (Atlantic mackerel); Scylla serrata (mud crab); Sepia plangon (squid); Sinularia dura (soft corals); Solaster endeca (starfish); Somniosus microcephalus (Greenland shark); Sphenodon punctata (tuatara); Spirobranchus giganteus (polychaete); Spisula solidissma (clam); Squalus acanthius (dogfish shark); Stichopus chloronatus (holothurian); Strongylocentrotus droebachiensis (sea urchin); Sus scrofa (pig); Tenebrio molitor (mealworm larvae); Tunica mogula (tunicate); Uca vomeris (fiddler crab); Vepricardium multispinosum (bivalve); Xenopus laevis (African clawed frog); Xestospongia exigua (sponge).

17 to 141 individuals were collected from 8 populations of the fished holothurian species Holothuria scabra (Echinodermata: Holothuroidea), from north-east Australia, the Torres Strait, and the Solomon Islands and investigated by allozyme electrophoresis of 7 polymorphic loci.Two shallow populations of Holothuria scabra were sampled in the area of Hervey Bay (Urangan, Tin Can Bay) in south Queensland during June 1998. Individuals from a deeper population in Hervey Bay (18-20 m) were obtained during 3 trawl shots using commercial prawn-trawling equipment.One intertidal population was sampled ca. 800 km north Upstart Bay in 1998. Data from these samples were used in a previous study investigating the relationship between 2 colour morphs and the gene flow between deep and shallow populations. This population was re-sampled in May 2000 to investigate whether gene frequencies and the small size of individuals (as found in 1998) were stable over time.During August 1999, samples were obtained from 2 reefs in the Torres Strait at the northern end of the GBR (Warrior Reef, Dungeness Reef). Two locations in the Solomon Islands, Kohinggo Island (Solomon Island A) and Kolombangarra Island (Solomon Island B), were sampled in December 1999.Samples from intertidal populations were taken during low tides by walking on the mud flats. During these periods, holothurians in shallow tide pools, usually with at least a sparse seagrass cover, migrate to the surface of the sediment. Since large areas had to be covered to obtain sufficient individuals, no effort was made to obtain subsamples within each of the populations. The length of all individuals was recorded to the nearest centimetre. A subsample of the gut lining (cleaned from sediments) was snap frozen in liquid nitrogen for later analyses.Seven polymorphic enzyme loci were surveyed using allozyme electrophoresis: PGM, HK, GPI, MDH, PEP-1, PEP-2 and PEP-3. Full details of staining and electrophoresis methods are given in:Ballment E, Uthicke S, Peplow L, Benzie JAH (1997) Techniques for enzyme electrophoretic analysis of the holothurians Holothuria atra and Stichopus chloronotus (Holothuroidea: Aspidochirotida). Aust Inst Mar Sci (AIMS) Tech Rep Ser 27:1-47Basic analyses of genetic variability were carried out using programs in the BIOSYS-1. F-statistics, cluster analyses and tests of conformation to Hardy-Weinberg expectations were performed using the TFPGA package. The contribution of asexual reproduction to each population was calculated as described in detail in:Uthicke S, Benzie JAH, Ballment E (1998) Genetic structure of fissiparous populations of Holothuria (Halodeima) atra on the Great Barrier Reef. Mar Biol 132:141-151. Deviations from Hardy-Weinberg equilibrium for each locus at each reef were tested by an exact-test, using the conventional Monte Carlo method with the default settings in TFPGA. To test for evidence of isolation by distance, Mantel¿s tests were performed on transformed (log + 1) geographic distance (km) and Rogers' genetic distances. The significance of Mantel's normalised Z was tested by 10000 random permutations using NTSYS-PC software. The aim of the study was to investigate gene flow between populations separated by different geographic scales (~20-2000 km), along the north-east coast of Australia, Torres Strait and the Solomon Islands, to provide information on connectivity to assist management and add to fundamental knowledge on the biology of this ecologically and economically important species.

In August/September 1993, surveys of coral community composition and structure were carried out at Scott Reefs (North Scott Reef and South Scott Reef) and two reefs in the Rowley Shoals group (Mermaid Reef and Clerke Reef).Coral communities were surveyed at a total of 94 sites, using a semi-quantitative visual survey method and a subset of these sites were surveyed using a video belt transect technique. Sites were areas of around 100-300 m², arranged along cross-reef profiles on the reef flats in a depth range of 0.5-2 m and on the slopes or adjacent reef floor at 4-6 m and 8-12 m. Aerial photography was used to assist in selection of study areas.During each visual survey a detailed list of coral species was made and the relative abundance of each taxa, as a percentage of total macro-benthos, was estimated. The site descriptors recorded were maximum and minimum depth (measured); and subjective estimates of the following: slope; percentage cover of hard substrate; percentage cover of major benthic groups (hard coral, soft coral, macro algae and sponge); percentage cover of substratum categories (platform; large blocks; small blocks; rubble; gravel; sand). An additional 4 sites were surveyed, without recording detailed species lists.A Sony Hi 8 video camera was used to film five replicate 20 m long belt transects about 40 cm wide, within each of the 3 depth ranges, in a sub-set of the sites used for visual surveys. Estimates of percent cover of hard coral, soft coral, algae and bare substratum were made using point sampling of the video tape. At 25 regularly spaced pauses along each video tape, the identity of each item under five points marked on the screen of the TV monitor (one near each corner and one in the centre) was recorded. Percent cover estimates were used to estimate the heterogeneity of the bottom cover as a basis for designing an appropriate sample protocol for a future monitoring program. The visual surveys were carried out to determine whether recognisable, taxonomically consistent assemblages of coral species occurred at the shallow water study sites and to determine the approximate spatial extent of these corals. The surveys were also used to provide detailed taxonomic descriptions of the coral communities at the sites where the video transects were recorded. These surveys were the first quantitative assessments of coral community structure on northwest Australian offshore reefs, previous coral surveys being largely concerned with taxonomic and biogeographic problems.The information collected during this survey formed the basis of of site selection for the subsequent long-term monitoring project.

Experiments were conducted to determine whether larger benthic foraminifera is prone to bleaching caused by increases in temperature and nutrient levels. The experiments aimed to characterise the physiological stress threatening these species, predicted to occur on tropical reef waters in the near future. Nutrient levels were chosen to represent naturally occurring nutrient concentrations during flood-plume events on the GBR, and temperatures were chosen to reflect current and future predictions for the GBR (Lough et al. 2006; Lough 2007). Specimens of Amphistegina radiata and Heterostegina depressa were collected during dry season 2009 and wet season 2010, from the Whitsundays area nearby sites Double Cone Island, Border Island, Deloraine Island and Edward Island. Calcarina hispida specimens were collected from Heron Island 2009 and Calcarina mayorii from Magnetic Island. Daily average SST was obtained from AIMS AWS stations at Hardy Reef and Heron Island, temperature logger are Nelly Bay. Additional samplesof A. radiata and H. depressa were collected from Dent Island and Bait Reef. A 6 day experiment with temperature manipulation were carried out with five individually set temperatures 23, 28, 30 32 and 33, exposing samples of A.radiata, H. depressa, and C. hispida. These experiments were repeated three times for A. radiata and H. depressa. To avoid thermal shock, the specimens were gradually introduced to the five different temperature treatments. Subsequent experiments used light levels of 11 -15 µmol photos m-2 s-1. A 30-day flow-through experiment was conducted where the effects of three temperature ranges and three nutrient levels were studied simultaneously: Temperature: 26, 29 and 31, and nutrient concentrations of 0.5, 1.0 and 1.4 µmol L-1. Specimens of A.radiata and H.depressa contained in six-well plates, and C. mayorii was contained in polypropylene tubes. Analysis included photosynthetic efficiency, Chl a, motility and growth measurements in A. raditata. Results of these experiments suggested that physiological stress and bleaching are species specific. This research was supported by the Australian government’s Marine and Tropical Sciences Research Facility, implemented by the Reef and Rainforest Research Centre in northern Queensland, Australia.

A weather station buoy was deployed on the northern side of Wistari Reef. Deployment Details: Date deployed: 20/10/89 (SGBR2) Date recovered: 25/10/89 (SGBR2)Instrument: Weather Station #721Sensors: wind speed, wind direction This deployment was a component of the SGBR Project 1989-1990.

Comparisons of leaf turnover by crabs (Sesarma messa) and microbes were carried out at Chunda Bay. Yellowing leaves of Rhizophora stylosa, which were about to fall, were collected. Ten leaves were retained, dried, weighed individually, ashed at 500°C for 24 hours and reweighed to calculate a conversion factor from fresh weight to ash-free dry weight (AFDW). Groups of four leaves were weighed and placed in nylon bags with a 2 mm² mesh size. Single leaves were weighed and 1m lengths of nylon twine were attached to the petiole.Bags (restricting access to leaves by crabs) and individual leaves (allowing access by crabs) were tied to the forest floor within the low intertidal region of a Rhizophora forest at two sites, 100m apart. At intervals of 2 and 6 weeks, three replicates of each treatment were removed from each site. Leaves were cleaned of sediment, dried, weighed and ashed.Measurements of removal of leaves by crabs and leaf litter fall were made on five occasions between April 1985 and January 1986 at Coral Creek in Missionary Bay, Hinchinbrook Island. On each occasion, leaf removal experiments were conducted during both day and night low tide periods. Six 25 m² plots were marked out in the low to mid-intertidal zone of the mixed Rhizophora forest. Sixteen litter catchers were deployed randomly around the experimental plots on each sampling occasion. All litter was removed after 7 days, dried at 100°C for 3 days, sorted into components and weighed.Yellowing leaves of Rhizophora spp. were collected and the area of each leaf measured with a Lambda Area Meter. A 1m length of nylon twine was tied to each petiole. At the beginning of each low tide period, all leaves on the surface of each plot were removed and then a number of the measured leaves were tethered within each plot. All tethered leaves were retrieved after 6 hours and a record was made of whether the leaf had been taken down a crab hole. Additional leaves falling into each plot were also collected. The surface area of each tethered leaf was measured and the loss of leaf area converted to dry weight loss using a pre-established relationship between surface area and dry weight. The area of leaf lost to crabs was visually estimated for the additional leaves falling into each plot.In January 1986, modified leaf removal experiments were carried out in other areas of mixed Rhizophora forest at an additional site at Coral Creek as well as Priest Creek and First Creek in Missionary Bay. This research was conducted to collect quantitative measurements of the rates of mangrove leaf burial and consumption by crabs. This is an additional pathway of leaf litter processing that should be included to mangrove food chain models.

A survey of the Keep River, Northern Terrritory was undertaken on the 17th and 18th October 2001. On the first day, 5 CTD casts were done between 0935 and 1150 hrs at the gauging station. CTD casts were also done at a further 3 stations along the river. Floc photographs were taken at CTD sites. A CTD, logging at 1 min intervals was deployed on the second day to collect data for the rising tide.A total of 20 water samples were collected from the CTD sites and analysed for NH4, PO4, NO2+NO3, NO2, and Si. This preliminary survey was undertaken in response to concerns over the possible effects of the Ord River Irrigation Area Stage 2 (M2 Supply Channel) on the Keep River. The project area included the lower reaches of the Keep River and Sandy Creek catchments and a transfer of water from the Ord River to the Keep River catchment was planned. At the time, the estuarine dynamics of the Keep River were largely unknown. No further work was done by AIMS in this river system.

The coral, Acropora millepora and the crustose coralline algae, Neogoniolithon fosliei were exposed to 3 photosystem II (PSII) herbicides (diuron, hexazinone and atrazine). Corals were collected at depths between 1 and 3m from Double Cone Island and Hayman Island in the Whitsunday group. The crustose coralline algae was collected from Davies Reef at depths between 5 and 7m.Experiments assessed the effects of the variables temperature (26, 30, 31, 32 °C) in combination with 3 herbicide concentrations, and exposure duration (up to 7 days) on photosynthetic efficiency and bleaching. To examine the effects of the herbicides diuron, atrazine and hexazinone in conjunction with increasing temperatures on coral and crustose coralline algae.