An Aanderaa water level recorder was attached to mooring CM2, located south of John Brewer Reef and in the free stream. The mooring was deployed in 36m of water. Deployment Details:Date Deployed: 4/4/1987Date Recovered: 5/9/1987Instrument Deployed:Aanderaa WLR #W615Depth: 32m 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. Tide gauges were placed at the corners of the model (moorings CM1, CM2, CM4 and TG1) and in the centre of the model, close to John Brewer Reef (TG2). The mooring CM1 drifted from its original position and only data up to the 27/5/87 are considered reliable. Mooring CM4 drifted to the Whitsunday Islands and the data were not considered reliable.

A 20 month study of zooplankton at three stations located across the transition zone between coastal and offshore waters in the central Great Barrier Reef lagoon was undertaken.The abundance and egg production rate of constituents of the zooplankton assemblage characteristic of the coastal zone rapidly increase subsequent to events such as flooding and upwelling. Sampling spanned two summer monsoonal seasons, the first of which (1990-91) was very wet. The second monsoonal season (1991-92) was very dry and was characterised by intrusive upwelling events from the Coral Sea. Chlorophyll a concentrations did not rise in the wet year, probably because of light limitation, but did rise as a result of upwelling. Terrestrial run-off in the wet year had a greater apparent effect on zooplankton abundance patterns than did upwelling in the dry year, except where coastal trapping allowed sufficient time for increases in zooplankton abundance to occur. Egg production rates by the copepods Acrocalanus gibber and Acrocalanus gracilis showed haphazard spatial differences. Nitrogen-specific egg production ranged between 0.03 and 0.21/day for Acrocalanus gibber, and between 0.13 and 0.41/day for Acrocalanus gracilis. The egg production rate by Acrocalanus gibber was food limited for most of the year and showed a poor correlation with temperature. This research was undertaken to examine the effects of the interaction between coastally trapped water and offshore water on zooplankton community structure and production.

Three trips were made to Cape York to sample fish in estuarine and low-wooded island mangrove habitats:Trip 1 (December 1995): Jacky Jacky Creek, Olive River, Lockhart River, McIvor River, Night Island Trip 2 (February 1996 - wet season): McIvor River, Lockhart River, Pascoe River, Escape River, Jacky Jacky CreekTrip 3 (June 1996 - dry season): Jacky Jacky Creek, Escape River, Bird Islands, Pascoe River, Lockhart River, King Island, McIvor River, Port Douglas.Water quality parameters were measured at all locations. These included NH4, NO3, TDN, DON, PON, PO4, TDP, DOP, POP, SiO, Chlorophyll a, Phaephyton and suspended solids.In Jacky Jacky Creek, Escape River, Pascoe River, Lockhart River and the McIvor River, fish were sampled with groups of monofilament gill nets, each 33 m long by 4.5 m deep, with stretched mesh sizes of 152, 102 and 51 mm. Multi-panel nets, 30 m long by 2 m deep, with stretched mesh sizes of 19, 25 and 32 mm were also deployed. Upstream sites (2-10km) from the mouth and downstream sites (within 1 km of the mouth) were sampled. Nets were set for up to 11 daylight hours. Catch was recorded on each hourly check by species, size and abundance. Most fish that were alive when removed from the nets were measured and released. Dead fish and unknown species were frozen and retained for identification and gut contents analysis. Food items were identified to general taxa and summarised by frequency of occurrence (percentage of all fish in a taxa having consumed a particular food item). Catch per hour of net deployment was calculated for each net set.At upstream and downstream sites, centered on net deployment stations, continuous measurements were taken using logging instrumentation while nets were in place. DataSonde Hydrolab units were used to track turbidity, oxygen, salinity, temperature and pH. A flow velocity meter (Starflow) was used to track water depth, flow rate and direction. Jacky Jacky Creek, Escape River, Pascoe River, Lockhart River and the McIvor River, were also classified according to bioregion, relative influence of tide at the entrance to the estuary, geomorphology, fishing exploitation, latitude (decimal degrees), direction of outfall and name of receiving waters, tidal range (m), water depth at mouth at midtide (m), salinity (ppt), water temperature (°C), composition of the estuary substrate, area of open water (km²), total area of mangroves (km²), width of estuary mouth (km), catchment area (km²), percent of catchment cleared, maximum elevation in the catchment (m) and average annual rainfall (mm). This study was undertaken to:1. quantify relationships between environmental characteristics of watersheds and the relative abundance and community structure of associated faunal communities in mangrove-dominated riverine estuaries of northeastern Queensland2. quantify relationships between environmental characteristics of offshore mangrove islands and the relative abundance and community structure of associated faunal communities on low-wooded islands of the Great Barrier Reef3. determine changes in faunal assemblages in riverine and low-wooded islands over time by comparing past and current surveys, and to provide an opportunity for future comparisons by establishing baseline information4. identify and compare trophic relationships in a variety of mangrove ecosystems5. develop a model for relating the conditional of mangrove faunal assemblages to environmental conditions toward the ultimate goal of predicting the potential impacts associated with proposed developments and resource users. Some of these data are used in the publication:Ley JA (2005) Linking fish assemblages and attributes of mangrove estuaries in tropical Australia: criteria for regional marine reserves. Marine Ecology Progress Series 305: 41-57.

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.

Predator exclusion experiments, using laboratory reared juvenile crown-of-thorns starfish (Acanthaster planci), were carried out in an area of dead coral rubble on the leeward side of Davies Reef, at depths between 12 and 15 m. One month post settlement starfish were deployed in February 1991, while 4 and 16 month old starfish were deployed in May 1991 and 7 month old starfish were deployed in August 1991. Three different sized plastic boxes with tight fitting lids were prepared for the different age groups of starfish and the lids and sides of the boxes were covered with mesh. After deployment, the mesh on the boxes was cleaned every 1 to 2 days to remove silt and the adequacy of water flow through the mesh was tested periodically.Starfish were placed in boxes with either a natural rubble treatment or a control rubble treatment. The natural rubble treatment consisted of pieces of unconsolidated dead coral rubble, complete with algal and motile epifaunal assemblages, which were collected directly from the seabed at the time of deployment. The control rubble treatment was made up of sun bleached or beach collected coral rubble, which was conditioned in flow-through aquaria for several weeks to allow algal and epifaunal assemblages to develop.Ten boxes of each of the control rubble and natural rubble treatments were used for the 1, 4, and 7 month old starfish, while 5 natural rubble treatments only were used for the 16 month old starfish. In addition, 5 replicate open boxes (natural rubble treatment, without lids) were deployed with 7 month old starfish, allowing free movement of the starfish and predators in and out of the boxes. Open boxes containing 1, 7 and 16 month old starfish were deployed inside larger boxes as escape controls and on recovery the numbers of starfish which had moved to the outer boxes were counted. The number of starfish placed in each box was dependent in the age class of the starfish and the number of starfish available in each age class.The boxes were recovered after 6, 13, 16 and 13 days for the 1, 4, 7 and 16 month old starfish respectively. The contents of each box were washed into bottles and fixed in mixture of buffered 10% formalin in seawater and Rose-Bengal stain. Prior to fixing, any starfish, which could be recovered alive were removed, counted and measured (greatest diameter). The fixed material was sorted by washing the rubble over 6, 1 and 0.1 mm mesh screens and then the rubble was individually washed over the mesh. All starfish were then recovered from the mesh screens and counted and measured. Other epifauna in the 1 mm screen were also counted and categorised with the aid of a dissecting microscope. This research was undertaken to investigate mortality rates of small crown-of thorns starfish. In these field experiments, the survival of small starfish living in their natural habitat was compared with that of starfish provided with similar food resources and shelter, but in the absence of potential predators or other hazards.

Benthic communities on coral reefs at locations in Florida, the Bahamas, the Turks and Caicos Islands and Haiti were surveyed in October 1972. This survey supplemented the extensive sampling of the reef terrace off Grand Bahama Island made possible due to having access, over several years, to the saturation diving facility, Hydro Lab. Observations were made along 10m line transects. The length occupied by each sessile organism and the distance between organisms were recorded in sequence. The total length of an individual species within a transect was used to calculate the percent cover of that species. A total of 46 transects were completed.Specimens were also collected and returned to the surface for identification to species level where possible. Research was undertaken to investigate and compare the little known benthic communities on submarine terraces within the Bahamian region. List of species or species groups identified along transects and used in data analyses (68 of 126):Briareum asbestinum (Pallas)Erythropodium caribaeorum (Duchassaing and Michelotti)Plexaura homomalla (Esper)Plexaura flexuosa LamourouxPlexaura sp.Pseudoplexaura porosa (Houtuyn)Eunicea palmeri BayerEunicea mammosa LamourouxEunicea fusca Duchassaing and MichelottiEunicea tourneforti Milne-Edwards and HaimeEunicea clavigera BayerEunicea knightii BayerEunicea calyculata Ellis and SolanderEunicea sp.Muriceopsis flavida (Lamarck)Plexaurella nutans (Duchassaing and Michelotti)Plexaurella grisea KunzePlexaurella fusifera KunzeMuricea muricata (Pallas)Muricea laxa VerrillMuricea elongata LamourouxPseudopterogorgia bipinnata (Verrill)Pseudopterogorgia kallos (Bielschowsky)Pseudopterogorgia rigida (Bielschowsky)Pseudopterogorgia americana (Gmelin)Pseudopterogorgia elisabethae BayerGorgonia ventalina LinnaeusStephanocoenia michelinii Milne-Edwards and HaimeMadracis decactis (Lyman)Acropora cervicornis (Lamarck)Agaricia agaricites L. forma agaricitesAgaricia agaricites L. forma carinataAgaricia agaricites L. forma purpureaAgaricia fragilis DanaAgaricia lamarcki Milne-Edwards and HaimeHelioseris cucullata (Ellis and Solander)Siderastrea siderea (Ellis and Solander)Porites astreoides LeseurPorites porites (Pallas)Porites furcata LamarckDiploria labyrinthiformis (Linnaeus)Manicina areolata (Linnaeus)Colpophyllia natans (Muller)Montastrea annularis (Ellis and Solander)Montastrea cavernosa (Linnaeus)Meandrina meandrites (Linnaeus)Dichocoenia stokesii Milne-Edwards and HaimeDichocoenia stellaris WellsDendrogyra cylindrus EhrenbergMussa angulosa (Pallas)Scolymia lacera (Pallas)lsophyllia sinuosa (Ellis and Solander)lsophyllastrea rigida (Dana)Mycetophyllia lamarckana Milne-Edwards and HaimeEusmilia fastigiata (Pallas)SpheciospongiaIotrochota birotulataGeodia gibberosa(Axinellidae)Verongia?Verongia?Ianthella ardis?Dasychalina cyathina?(other infrequent sponges)Millepora alcicornis(algae)Additional data collected in relation to these communities are described in the metadata record "Standing stocks of organic carbon associated with sessile reefal communities on submarine terraces in the Bahamian region".

These data consist of 20-point score estimates randomly placed on individual high resolution downward facing benthic digital images taken at Barracouta shoal using the AIMS towed video system. The AIMS towed video system comprises a towed camera platform sending a live camera feed to a vessel-based, realtime image classification system (see Heyward et al. 2011) and a downward-facing high resolution still camera and strobe system programmed to take sequential still images at fixed time intervals of 10 seconds. The towed platform was deployed over the stern of the vessel, maintained as near as possible within a metre of the seabed and towed at 1-2 knots (1.5 nominal). Transect lengths varied among the years of data collection. The downward-looking still images were geo-referenced during post-processing then analysed using a point-intercept approach. Information on benthic biota at each shoal was extracted from images using a point intercept approach with the AIMS Reefmon software (Jonker et al., 2008). All images were analysed using the Reefmon database system, with five overlaid points classified per photo and data logged against transect, depth and position. The data provided here are derived using a machine learning model trained using the original manual annotations. The artificial intelligence engine called BenthoBot was used to re-analyse all seabed images from all years 2010-2016, processing each image using exactly the same approach. BenthoBot is a computer algorithm developed to classify points on an image, based on the spectral properties extracted from each image. It has been developed specifically by the Australian Institute of Marine Science to providean efficient and consistent means of generating the point based broad scale benthic classification data. The benefits of using BenthoBot include standardisation of the number of points sampled per image across all years (20 points per image) and removal of inconsistency in point classification associated with numerous technicians scoring images that may cause spatial and temporal artifacts. Secondary (textural) datasets correlated with seafloor properties were developed from multibeam bathymetry to provide information on environmental characteristics, and are also provided here extracted for each image location as covariates.

The objective of WAMSI DREDGING SCIENCE NODE Project 4.3 was to better understand the relationship between TSS and the orbital motion of waves using the instrumentation used during the Gorgon dredging program, at multiple sites using the baseline (pre-dredging) data and then during the dredging program. Specifically, the objective was to predict TSS levels based on the orbital velocity of waves and to identify periods where the measured TSS levels are higher than the modelled data predicts and which therefore may indicate turbidity caused by dredging or spoil disposal and which could represent periods of high sediment deposition. The information from the sediment deposition sensor can then be used to verify periods of high(er) sediment deposition.. Data is in the form of a report, which is a secured (printable, non-editable), searchable, Portable Document Format (PDF) showing the results of the analyses.

Characterization of shallow water (A series of marked transects were established at multiple depths and locations around Seringapatam Reef. Six locations on the outer reef slope and adjacent reef flat, together with four within the reef lagoon. Where possible, these sites included and extended sampling locations previously surveyed by AIMS Heyward et al. (2010). A diver-based assessment of shallow reef habitats and an assessment of coral spawning condition, with funding from Conoco Phillips.

Plants were exposed to 6 concentrations of trifloxysulfuron for 28 days followed by 56 days of recovery after removal of the herbicide. During this time, assessments were made of appropriate parameters including shoot height, leaf number, fresh and dry weight. This study was designed to evaluate the effects of the sulfonylurea herbicide, trifloxysulfuron,on the growth of the mangrove Avicennia marina under tidal conditions. Data was analysed to detect significant deviations in these parameters from control values, and thus determine the NOAEC (no-observed adverse effect concentration).