AndreaBozzo/ceres-open-data-index huggingface dataset:
Herbert River Lucinda Jetty Turbidity Data Transect Monday 9th February 2004

The objective of the research reported in this thesis was to develop a technique to monitor the dynamics of sediments and nutrients entering the coastal ocean with river plumes associated with high intensity low frequency events (e.g. floods), using ocean colour remote sensing. The data collected included suspended sediment concentration (TSS) and turbidity profiles.

Tags: Oceans | Ocean Optics | Turbidity, concentration_of_total_suspended_sediments, depth, secchi disk depth, secchi_depth_of_sea_water, total suspended sediments, turbidity
Organization: Australian Ocean Data Network
ACCESS1-3 model output prepared for CMIP5 sstClimSulfate (Version 2015)

sstClimSulfate is an experiment of the CMIP5 - Coupled Model Intercomparison Project Phase 5
(http://cmip-pcmdi.llnl.gov/cmip5/). CMIP5 is meant to provide a framework for coordinated
climate change experiments for the next five years and thus includes simulations for
assessment in the AR5 as well as others that extend beyond the AR5.
6.4b sstClimSulfate (6.4b sulfate aerosol forcing) - Version 1: AMIP-style experiment with control run climatological SSTs and sea ice (as in expt. 6.2a) but with aerosols consistent with conditions in year 2000 of the historical run (expt. 3.2)
Experiment design: http://cmip-pcmdi.llnl.gov/cmip5/docs/Taylor_CMIP5_design.pdf
List of output variables: http://cmip-pcmdi.llnl.gov/cmip5/docs/standard_output.pdf
Output: time series per variable in model grid spatial resolution in netCDF format
Earth System model and the simulation information: CIM repository
Entry name/title of data are specified according to the Data Reference Syntax
(http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf)
as activity/product/institute/model/experiment/frequency/modeling realm/MIP table/ensemble
member/version number/variable name/CMOR filename.nc.

Tags: 0399 - Other Chemical Sciences, 0401 - Atmospheric Sciences, 0405 - Oceanography, 0406 - Physical Geography and Environmental Geoscience, Atmospheric Sciences, National Computational Infrastructure (NCI), Oceanography, Other Chemical Sciences (Environmental Chemistry), Physical Geography and Environmental Geoscience
Organization: Australian Ocean Data Network
2016 SoE Marine Chapter - State and Trends - Crown-of-Thorns Starfish (COTS) outbreaks

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment The state and trends of ecological processes – Crown-of-Thorns Starfish (COTS) outbreaks.The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record.

DESCRIPTION OF ECOLOGICAL PROCESS FOR EXPERT ASSESSMENT
COTS (Acanthaster planci) are natural predators of coral and occur on all coral reefs in Australia’s marine domain.  High fecundity means that when spawning coincides with favourable conditions, resulting recruitment can lead to outbreak densities of large starfish that can deplete local coral cover within 3-5 years. Populations then collapse through starvation and disease but not before they spawn abundant planktonic offspring, which may form secondary outbreaks on downstream reefs. There have been four synchronised eruptions of secondary outbreak in the highly connected, archipelagic Great Barrier Reef (GBR) since 1960. In the subsequent 15-20 years, multi-generational waves of secondary outbreaks have progressed southward through the central GBR. Average coral cover on GBR reefs fell by half over  27 years of monitoring to 2012; about 40% of the total decline was attributed to COTS.  Outbreaks have also been recorded in all other parts of the starfish’s Australian range (Far northern GBR, Torres Strait, northwest WA), but their significance is uncertain since systematic monitoring was only recently implemented or is non-existent. 
DATA STREAM(S) USED IN EXPERT ASSESSMENT
The assessment is based on data and analysis published in peer reviewed literature and unpublished reports. Details of specific data sets used to generate the assessment have not been provided.

2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details]
• 2016 •
Assessment grade: Poor
Assessment trend: Unclear
Confidence grade: Adequate high quality evidence and high level of consensus
Confidence trend: Adequate high quality evidence and high level of consensus
Comparability: Grade and trends are somewhat comparable to the 2011 assessment
• 2011 •
Assessment grade: Good
Assessment trend: Stable
Confidence grade: Limited evidence or limited consensus
Confidence trend: Adequate high quality evidence and high level of consensus

CHANGES SINCE 2011 SOE ASSESSMENT
Since the 2011 assessment there has been widespread outbreaks of COTS detected across its range. There is a general lack of information with which to determine long term trends and so trends are regarded as unclear rather than stable.

Tags: echinodermata, expert assessment, grazing, predation
Organization: Australian Ocean Data Network
WAMSI 2 - Dredging Node - Project 5.1.2 - Seagrasses of the North West of WA: biogeography and considerations for dredging-related research

This project (5.1) is comprised of two literature reviews. This is the second review and summarises what is known on the biogeography, ecology, ecosystem function and biology of seagrasses from the north-west of Western Australia.

Tags: Angiosperms, Biosphere | Aquatic Habitat | Benthic Habitat, Dredging, Oceans | Coastal Processes | Sediment Transport, Oceans | Marine Biology | Marine Plants, Oceans | Marine Sediments | Turbidity, Oceans | Water Quality | Light Transmission, Thresholds
Organization: Australian Ocean Data Network
Mangroves and Mangrove Birds of Western Australia

Mangroves and Mangrove Birds of Western Australia . Eighty- three blocks of mangroves were visited in Western Australia from Cambridge Gulf to Shark Bay between 1973 and 1982.The vegetation and substrate at each site are described. Twenty-two species of bird were found to be confined to mangroves or limited to them for at least part of their range. For each species, data are given on distribution, status, ecology, voice, food, breeding, colour of unfeathered parts, and for some species notes on geographic variation and taxonomy.

Tags: Biosphere | Vegetation | Vegetation Species, Biosphere | Zoology | Birds, Breeding, Distribution, Oceans | Coastal Processes | Mangroves, States, Territories (Australia) | Western Australia, Taxonomy
Organization: Australian Ocean Data Network
Derwent Estuary Recreational Water Quality monitoring program -Little Sandy Bay South

Little Sandy Bay South monitoring site is collected as part of the Derwent Beach Watch program. Derwent Beach Watch is a collaborative program between councils and state government that tests water quality at 18 swimming sites around the estuary during summer months. 
Water samples are collected each Tuesday from the start of December to the end of March and analysed for the faecal indicator bacteria Enterococci (Enteralert method) at the Public health Lab. Because the samples must be cultured, it takes several days to publish the results.

Tags: Derwent Estuary, Hydrolab Vertical Profiler, Oceans | Salinity/density | Salinity, Oceans | Water Quality | Contaminants, Oceans | Water Quality | Ph, Oceans | Water Quality | Turbidity, Oceans | Water Quality | Water Temperature, Water Quality Monitoring, sea_water_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
Temporal patterns of plastic contamination in surface waters at the SS Yongala shipwreck, Great Barrier Reef, Australia

Marine plastic pollution is an identified contaminant of emerging concern, with expected increases in contamination levels if plastic production projections eventuate. Scientists, managers and the public are increasingly interested in understanding the status and temporal trends of plastic contamination in the marine environment and specifically the Great Barrier Reef (GBR). Presented in this study is the first temporal assessment of plastic contamination in the surface waters of the GBR, Australia. This was accomplished by conducting replicate surface seawater samples (n=66) adjacent to the SS Yongala shipwreck (central GBR), in Bindal sea country, between 2016 and 2019 using a neuston net. The processing workflow included a stringent protocol involving density flotation, filtration, visual identification and sizing of putative plastics using stereomicroscopy, and chemical characterisation using Fourier transform infrared spectroscopy (FTIR). Overall, a total of 533 plastic items were identified and confirmed as plastic, with plastics detected in every single replicate tow, bar one. Polyethylene and polypropylene were the most common polymers present, and were comprised of macro-, meso- and microplastic fragments and fibres. Concentrations of plastic fluctuated across the three years, with spikes related to wind-speed and extreme weather events. However, overall plastic trends did not significantly increase or alter throughout the study period. This study reveals the chronic presence of plastic debris in the surface waters of the central GBR and highlights the need for long-term monitoring of the marine environment for plastic contamination.

Organization: Australian Ocean Data Network
Peptides that inhibit neuronal nitric oxide synthase

Neuronal nitric oxide synthase (nNOS) inhibition tests were carried out on peptides in addition to other bioactivity experiments, in particular, antibiotic activity. Inhibition of nNOS was measured by monitoring the conversion of [3H]arginine to [3H]citrulline.Information recorded: individual identifier for sample, peptide sequence, molecular weight, stock concentration (mg/ml), source (native peptide, synthetic derivative), solvent and concentration.
 To test whether the peptides inhibit nNOS.
 Peptides tested: aurein, caerin, citropin, cupiennin, dahlein, frenatin, lesueurin, rothein, signiferin, uperin.Sources of native peptides: Cirinia signifera; Cupiennius salei; Litoria aurea, L. caerulea, L. citropa, L. chloris, L. dahlii, L. electrica, L. gilleni, L. gracilenta, L. infrafrenata, L. lesueuri, L. rothii, L. rubella, L. splendida, hybrid L. caerulea/splendida; Uperoleia mjobergii.The first report of neuronal nitric oxide synthase inhibition by a component of a spider venom (Cupiennius salei).Subsets of the data have been used in a number of studies.

Organization: Australian Ocean Data Network
OSU Buoy Group: Oregon Continental Shelf WISP current records

Data from moorings that were in place for at least 6 months in deep water and include meteorological data, pressure records and temperature records gathered by the Oregon State University (OSU) Buoy Group over a span of more than 35 years. In addition, included are a number of electronic (i.e., browser-formatted) data reports.
This dataset relates to current meter records from the Oregon shelf WISP mooring and includes early moorings at Sunflower, a WISP mooring, during the months prior to the actual beginning of WISP.
Other links available on this site will take you to the collection of data reports, an historical retrospective of the Buoy Group and instructions on how to download the data for the following:

Atlantic Ocean data
Pacific Ocean data
Indian Ocean data
Southern Ocean data 
Electronic data reports
History of the Group
How to use this disk


Tags: Buoy world ocean, Deep water mooring, Oceans | Bathymetry | Water Depth, Oceans | Ocean Pressure | Sea Level Pressure, Oceans | Ocean Pressure | Water Pressure, Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Conductivity, Oceans | Salinity/density | Salinity, PACIFIC OCEAN, beam_attenuation_coefficient, direction_of_sea_water_velocity, sea_water_electrical_conductivity, sea_water_pressure, sea_water_speed, sea_water_temperature, sea_water_u_velocity, sea_water_v_velocity
Organization: Australian Ocean Data Network
Effects of mesh size and diel variability in fish trap catch in the central Great Barrier Reef

In June/July 1991, a broadscale survey was undertaken across replicate mid-shelf reefs (Lodestone Reef, John Brewer Reef and Rib Reef) in the central Great Barrier Reef, in order to examine the effects of reefs, diel variability and mesh size on the performance of fish traps. In October 1991, trapping was undertaken at Lodestone Reef to examine in detail the effect of mesh size and diel variability on the performance of fish traps with time.Four commercially available mesh sizes were used in the initial survey. Each trap was individually covered with only one mesh size: 12.5 mm square, 30 mm hexagonal, 40 mm hexagonal, or 50 mm hexagonal mesh. In the second survey the 12.5 mm square mesh, which had proved unsuccessful, was not used.Traps were baited with approximately 1 kg of mulched Western Australian pilchards (Sardinops neopilchardus), placed in crab pot style bait canisters. Traps were set a minimum distance of 50 m apart and ranged up to a several hundred metres apart in order that the capture fields of each trap would not overlap. Traps were set sequentially by mesh size, randomly across the back reef habitat of all reefs in depths between 20 and 40 m.All trap setting was undertaken between 07:00 and 18:30 h. 'Night' set traps were hauled from 0700h onwards, with total soak times varying from 10 to 14 hours. Sorting and processing of trap catches was usually completed by 1000h. 'Day' sets were hauled from 1530h onwards, with total soak times varying between 6 and 9 hours. Sorting and processing was usually completed by 1830h and traps redeployed. The catch from each trap was placed in bins of running seawater. Each fish was identified to species and measured to the nearest millimetre (standard length, length to caudal fork, and body depth).
 Trapping surveys were undertaken to select the optimal mesh size for fish traps to be used in ecological studies of lutjanids and lethrinids. Surveys were also designed to determine if there were differences in catches between day and night and at different reefs.

Organization: Australian Ocean Data Network
Coastal Lake Assessment and Management Tool (CLAM): Queens Lake, Port Macquarie - Hastings Council

The Coastal Lake Assessment and Management (CLAM) tool allows stakeholders to assess the social, economic and environmental trade-offs associated with development, remediation and use options for coastal lakes and estuaries. Researchers at the Australian National University (ANU) developed CLAM in 2004 when contracted by the NSW State Government to provide sustainability assessments of 8 coastal lakes. Several projects have since been established directly with local government and NRM groups.
To date, 27 CLAMs have been developed in New South Wales, where they generally fit within estuary management or catchment management plans. To develop these CLAMs and build local capacity to maintain them, ANU-Enterprise Pty Ltd - the commercial company of ANU developed an Accreditation Scheme whereby local consultants are trained in the CLAM approach.

Tags: Agriculture | Agricultural Aquatic Sciences | Aquaculture, Agriculture | Agricultural Aquatic Sciences | Fisheries, Agriculture | Agricultural Plant Science | Reclamation/revegetation/restoration, Agriculture | Forest Science | Forest Fire Science, Agriculture | Forest Science | Reforestation, Biosphere | Aquatic Habitat | Coastal Habitat, Biosphere | Aquatic Habitat | Estuarine Habitat, Biosphere | Aquatic Habitat | Lakes, Biosphere | Aquatic Habitat | Rivers/stream Habitat, Biosphere | Aquatic Habitat | Saline Lakes, Biosphere | Terrestrial Ecosystems | Agricultural Lands, Biosphere | Terrestrial Ecosystems | Wetlands, Biosphere | Wetlands | Estuarine Wetlands, Biosphere | Wetlands | Riparian Wetlands, Human Dimensions | Economic Resources | Agricultural Economics, Human Dimensions | Environmental Impacts | Eutrophication, Human Dimensions | Environmental Impacts | Reclamation/revegetation/restoration, Human Dimensions | Environmental Impacts | Sewage, Human Dimensions | Environmental Impacts | Urbanization, Human Dimensions | Environmental Impacts | Water Management, Human Dimensions | Land Use/land Cover | Land Management, Hydrosphere | Surface Water | Lakes, Hydrosphere | Surface Water | Rivers/streams, Hydrosphere | Water Quality | Nutrients, Land Surface | Erosion/sedimentation | Suspended Solids, Land Surface | Landscape | Landscape Management, Oceans | Coastal Processes | Estuaries, Oceans | Coastal Processes | Lagoons, Oceans | Coastal Processes | Mangroves, Oceans | Coastal Processes | Sea Level Rise, Oceans | Coastal Processes | Shorelines, Queens Lake
Organization: Australian Ocean Data Network
Symbiodinium diversity on the Great Barrier Reef (MTSRF Project 2.5i.3)

Samples of S. flexibilis were collected from a total of 11 sites from inshore and offshore reefs within the Torres Strait, Cairns, Townsville and Whitsunday regions of the Great Barrier Reef between December 1998 and February 2000. The microsatellite alleles of Symbiodinium C (loci SymC_3-01, SymC_3-02,SymC_3-03 and SymC_3-04) were analysed for their genetic diversity using the variables inshore/offshore reefs; molecular variance pairwise estimates (FST) of genetic differentiation; and hierarchical cluster analysis of Euclidean distances of frequencies grouped using the UPGMA (Unweighted Pair Group with Arithmetic mean) algorithm.
 Site locations:Torres Straits (Dungeness); Cairns (Agincourt, Escape, Pickersgill and Undine Reefs); Townsville (Great Palm and Orpheus Islands, Rib and Trunk Reefs); Whitsunday (Hook and Deloraine Islands).

Organization: Australian Ocean Data Network
ROV Surveys of Scott Reef from the RV Falkor

In NW Australia a range of emergent reefs bound the western margin of the Oceanic Shoals bioregion, but with the major feature being numerous submerged shoals lying along and across the shelf edge. Scott Reef, the largest emergent reef system, has a diverse shallow water coral reef ecosystem that has demonstrated impressive resilience to cyclone and coral bleaching disturbances over the last 15 years (Gilmour et al, 2013). The adjacent deeper lagoon of South Scott Reef covers approximately 300 km2 in depths of 30-­?70m. This deeper lagoon has areas of very high live coral cover and represents the largest example of a mesophotic reef system in the region. The slightly deeper distribution of these habitats appears to have ameliorated those impacts such as thermal stress and cyclones, which have caused significant disturbance to the adjacent shallow areas. 
A spatial model using multibeam and seabed surveys with towed video and AUV in 2009 and 2011 has been developed by AIMS to describe and predict the distribution of the key mesophotic habitats. While this model is the most advanced of its type for such a reef system, additional research suggests that fine?scale water movement, including turbulence and upwelling driven by internal waves, may be a key driver of these habitat patterns. We used the RV Falkor’s time at Scott Reef to characterise these detailed oceanographic processes with the goal of integrating the physical and biological data to further develop the spatial model, then extend this approach to other reefs and shoals in the region. The fine scale hydrodynamics and their relationship to patterns of seabed biodiversity was explored from RV Falkor with intensive oceanographic measurements of the water column across these features and detailed imaging transects of the seabed habitats using the SOI DDROV and other camera gear.

Organization: Australian Ocean Data Network
Feeding on sponge exudates by a holothuroid at Davies Reef, Great Barrier Reef

In the lagoon at Davies Reef, the substrate was cleared around a large specimen of the sponge, Ianthella basta located at a depth of 20m. All specimens of the holothuroid, Synaptula lamperti were removed and the sponge was enclosed in a polythene bag containing glucose and proline labelled with tritium and incubated for 2.5 hours. After incubation, 81 Synaptula lamperti were returned to the sponge and 5 were retained as a control for background radiation. Five Synaptula lamperti were removed from the sponge after 2, 4, 8, 19.5, 28, 43, 52.5 and 67 hours and dissected into gut and body wall components. Three small pieces were cut from the sponge before the addition of labelled material and at 4, 19.5, 52.5 and 67 hours after returning the holothuroids to the sponge. All tissue samples were frozen and later digested and assayed for radioactivity.The 41 holothuroids remaining on the sponge were removed for chemical extraction. Soxhlet extractions of sponge and holothuroid tissues were made using organic solvents and then chromatographically fractionated.To determine whether sponges provided protection to holothuroids against predation, equal numbers of Synaptula lamperti were placed on Ianthella basta and on artificial sponges made of hessian, placed neaby. The experiment was conducted at two depths (5 and 17m) and survival after 1 and 5 days was recorded.
 This research was undertaken to determine if the holothuroid, Synaptula lamperti, was ingesting exudates directly from the sponge, Ianthella basta. This was investigated by radiolabelling sponge tissue and later examining the holothuroids for evidence of transfer of labelled material. Experiments were also conducted to determine whether the holothurians used the sponge for protection against predators.

Organization: Australian Ocean Data Network
ACCESS1-3 model output prepared for CMIP5 rcp85

rcp85 is an experiment of the CMIP5 - Coupled Model Intercomparison Project Phase 5 ( http://cmip-pcmdi.llnl.gov/cmip5/ ). CMIP5 is meant to provide a framework for coordinated climate change experiments for the next five years and thus includes simulations for assessment in the AR5 as well as others that extend beyond the AR5.
4.2 rcp85 (4.2 RCP8.5) - Version 1: Future projection (2006-2100) forced by RCP8.5. RCP8.5 is a representative concentration pathway which approximately results in a radiative forcing of 8.5 W m-2 at year 2100, relative to pre-industrial conditions. RCPs are time-dependent, consistent projections of emissions and concentrations of radiatively active gases and particles.
Experiment design: http://cmip-pcmdi.llnl.gov/cmip5/docs/Taylor_CMIP5_design.pdf
List of output variables: http://cmip-pcmdi.llnl.gov/cmip5/docs/standard_output.pdf
Output: time series per variable in model grid spatial resolution in netCDF format
Earth System model and the simulation information: CIM repository
Entry name/title of data are specified according to the Data Reference Syntax ( http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf ) as activity/product/institute/model/experiment/frequency/modeling realm/MIP table/ensemble member/version number/variable name/CMOR filename.nc .

Tags: 0399 - Other Chemical Sciences, 0401 - Atmospheric Sciences, 0405 - Oceanography, 0406 - Physical Geography and Environmental Geoscience, Atmospheric Sciences, National Computational Infrastructure (NCI), Oceanography, Other Chemical Sciences (Environmental Chemistry), Physical Geography and Environmental Geoscience
Organization: Australian Ocean Data Network