AndreaBozzo/ceres-open-data-index huggingface dataset:
IMOS - Ocean Radar - Quality Control procedures for IMOS Ocean Radar Manual

This document is the IMOS Ocean Radar Facility quality-control and data user’s manual. The Ocean Radar facility is a component of Australia’s Integrated Marine Observing System (IMOS). The document contains the description of the data stream, the data products, the data formats and the data quality control procedures for real-time (RT) and delayed-mode (DM) data produced by the Facility.

Tags: Ocean Radar Facility, Integrated Marine Observing System (IMOS)
Organization: Australian Ocean Data Network
Small molecule antioxidants in marine organisms from the Great Barrier Reef, Japan and USA

Specimens of the zoanthid, Palythoa tuberculosa and the ascidian, Lissoclinum patella were collected using SCUBA from 2-4 m depth at Davies Reef in June 1990. Specimens were stored at -20°C until extracted. Coral trout (Plectropomus leopardus) were caught by handline at the same reef and the ocular lenses excised and frozen. Freeze dried red alga samples were sourced from 2 locations: Porphyra tenera was a gift from the Yamamoto Nori Research Institute, Ota-ku, Tokyo, and Mastocarpus stellatus, collected from Schoodic Point, Maine, USA, was provided by Professor JM Shick.Methanolic aqueous extracts containing mycosporine-like amino acids (MAAs) were prepared from tissue samples from each species and the MAAs were separated and quantified by reverse-phase, isocratic high-performance liquid chromotography (HPLC).Phosphatidylcholine peroxidation inhibition assay (PC-assays) were conducted using 2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH) and soybean phosphatidylcholine (PC) as radical inititor and lipid substrate, respectively.AAPH-initiated oxidation reactions of MAAs in sample tissue extracts were conducted without phosphatidylcholine as a competing substrate.Mycosporine-Gly was fractionated from the Palythoa extract and after processing was quantified by photometric analysis using published molar absorptivity data. The antioxidant activity of mycosporine-Gly was determined with the addition of appropriate quantities of sample to give 15 and 30 µM concentrations of mycosporine-Gly in the PC-assay. Ascorbic and uric acids were used for comparison of PC peroxidation inhibition rates.In these sample extracts, mycosporine-glycine was reactive to peroxyl radicals whereas iminomycosporine-like amino acids (shinorine, porphyra-334, palythine, asterina-330 and palythinol) were oxidatively robust. Purified mycosporine-glycine inhibited peroxyl radical-initiated autoxidation of phosphaditylcholine in a concentration-dependent manner. These results suggest that mycosporine-glycine may function as a biological antioxidant in marine organisms.
 This research was undertaken to examine the antioxidant activities of extracts from tissues of different marine species by their peroxyl radical-trapping ability using the phosphatidylcholine peroxidation inhibition assay (PC-Assay).

Organization: Australian Ocean Data Network
Heron Island Sensor Float 1

A round 1.4m yellow buoy has been deployed in the Heron Island lagoon as part of the sensor network infrastructure at Heron Island in the southern Great Barrier Reef off Gladstone, Australia. The buoy is configured as a sensor-float with a Campbell Scientific logger, a spread-spectrum radio for communicating with the on-reef wireless network, a GPS and initially a surface mounted (30cm under the water surface) thermistor.The float is moored in the lagoon of Heron Island in around 3m of water and will be used to monitor the flow of water through the lagoon. It will be fitted with surface salinity and bottom depth and temperature in late 2008. The unit will be serviced every six months and will be used in the future for attaching new sets of sensors. The buoy is re-locatable and the GPS data should be used to find the current location.
 The buoy is one of five re-locatable platforms in the lagoon at Heron Island onto which sensor will be located. The buoys initially have a Campbell Scientific loggers powered off two 5W solar panels, a Garmin GPS unit and one thermistor located at the base of the buoy around 30cm below the water line. The buoys use a Campbell Scientific spread-spectrum radio to talk back to the base station located on Heron Island.
 Power SupplyBattery Backed (1 x 33Ahr AGM with Solar Regulator), 2 x 5W Solar Panel Supply.Logger Settings - Pakbus Address - 171Logger Setup as node (isRouter = False)CSDC7 comms board rate set at 34KCSD7 Beacon = 21600CSDC7 Neighbours range 1 - 1, 110 - 110, 120 - 120Over-Reef RF Network - RF411 attached to the CSIO port of the loggerRadio Settings - Active Interface - Datalogger CSDCSDC Address 7Protocol: Pakbus awareRadio Net Address - 0Hop Sequence - 0Power mode - less than 2mA 1 SecondRetry level - Low

Organization: Australian Ocean Data Network
IMOS - Ocean Gliders - Slocum glider deployment in Western Australia off Pilbara (July 2012)

The dataset contains temperature, salinity and biological parameters like for example dissolved oxygen and turbidity data measured by a Slocum glider in the region off Pilbara (Western Australia).
The Ocean Gliders Facility (formerly known as the Australian National Facility for Ocean Gliders (ANFOG)), manages Slocum gliders to be deployed on the continental shelf.
The variables available in this dataset are:
Temperature, salinity, conductivity, density, pressure, chromophoric dissolved oxygen matter, dissolved oxygen, fluorescence and backscatter coefficient at 660nm.

Tags: CTD (Conductivity-Temperature-Depth Profilers), Coloured Dissolved Organic Matter (CDOM), Countries | Australia, Fluorometers, Glider, IMOS Node | Bluewater and Climate, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Chemistry | Oxygen, Oceans | Ocean Chemistry | Suspended Solids, Oceans | Ocean Circulation | Ocean Currents, Oceans | Ocean Optics | Fluorescence, Oceans | Ocean Optics | Turbidity, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Conductivity, Slocum Glider, States, Territories (Australia) | Western Australia, concentration_of_coloured_dissolved_organic_matter, fluorescence_in_sea_water, mass_concentration_of_oxygen_in_sea_water, sea_water_electrical_conductivity, sea_water_pressure, sea_water_salinity, sea_water_temperature, volumetric_backscatter_coefficient
Organization: Australian Ocean Data Network
Colour changes associated with the semilunar cycle in the fiddler crab, Uca capricornis

The purpose of the experiment was to examine the colour changes associated with the semilunar cycle in the fiddler crab, Uca capricornis. Experiments were conducted in the East Point Reserve, Darwin from Nov - Jan (04/05 &amp; 05/06). 
1m diameter cages were constructed and stocked with 4 crabs of the species Uca capricornis. During one semilunar cycle, from one neap tide to the next, digital photographs were taken of 22 crabs (10 males, 12 females) active in the cages at approximately low tide. Photos were examined to observe any colour changes on a day to day basis. 
The results show that Uca capricornis do not rythmically change their colour or pattern between moults. Although some individuals did exhibit a slight variation, by brightening or darkening existing colours, there was no apparent trend in the number of crabs either brightening or darkening with respect to the time in the cycle.

Tags: 28 960036, Behavioural Ecology, Biosphere | Zoology | Crustaceans, Colour Pattern, Fiddler Crab, Ocypodidae, Semilunar Cycle, Uca capricornis
Organization: Australian Ocean Data Network
One Tree Island Sensor Relay Pole 3 (RP3)

A 6m steel pole has been installed within a small bommie in Third Lagoon on One Tree Island as part of the sensor network infrastructure at One Tree Island in the southern Great Barrier Reef off Gladstone, Australia. The sensor-relay pole provides a platform for the installation of sensors to measure and monitor water conditions within the lagoon of One Tree Island. The pole has real time communications using 900MHz spread spectrum radio back to a base station on One Tree Island. The pole is initially configured with a single thermistor string with six thermistors that is located down the outer wall of the bommie into the lagoon and so provides a temperature profile of the third lagoon of One Tree Island. The data is collected every 10 minutes and relayed via the base station to the Data Centre at the Australian Institute of Marine Science (AIMS).The system uses a Campbell Scientific logger into which the sensors are connected. The equipment is serviced every six months with plans to install additional instruments such as pressure and salinity. The pole is available for mounting of additional third part instruments and so forms an infrastructure to support future observational work at the Island.
 The Pole is one of three located in One Tree Island, one in each of the main sub-lagoons that make up the main lagoon of the reef. Each pole communicates with the other poles and back to the base station located on the Island using spread-spectrum radios, the base station currently uses a Telstra nextG connection back to the mainland and from there the data goes back to AIMS.The poles have a Campbell Scientific CR1000 logger into which the sensors are attached, the logger stores the data and then forwards it to the base station. The current sensors deployed include thermistor strings on each pole and a Vaisala WXT520 weather station on RP3.
 Power SupplyBattery Backed (1 x 33Ahr AGM with Solar Regulator), 4 x 5W Solar Panel Supply.Logger Settings - Pakbus Address - 230Logger Setup as router (isRouter = True)CSDC7 comms board rate set at 34KOver-Reef RF Network - RF411 attached to the CSIO port of the loggerRadio Settings - Active Interface - Datalogger CSDCSDC Address 7Protocol: Pakbus awareRadio Net Address - 0Hop Sequence - 0Power mode - less than 2mA 1 SecondRetry level - Low

Organization: Australian Ocean Data Network
Coastal Lake Assessment and Management Tool (CLAM): Coffs Creek, Coffs Harbour City 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, Coffs Creek, 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
Organization: Australian Ocean Data Network
2016 SoE Marine Chapter - Case Study - White shark status in Australasian waters

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 Case Study "White shark (Carcharodon carcharias) status in Australasian waters". The full Case Study, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Case Study are accessible through the "On-line Resources" section of this record.

DESCRIPTION OF THE FOCUS OF THE CASE STUDY
The white shark (Carcharodon carcharias) is a large, globally distributed, apex predator and one of the few shark species responsible for fatalities to humans. They are a target species for ecotourism, with the South Australian industry valued at over $6M annually. In Australian waters, it occurs from northwest Western Australia around the south coast to central Queensland as two populations separated east and west by Bass Strait. Biologically important areas for white sharks occur in all Marine Regions with the exception of the North Marine Region A geographically discrete nursery area spanning 65 km of coast is centred around Port Stephens in central New South Wales and a second more geographically extensive nursery area is present off 90 Mile Beach in southeast Victoria. Movements are extensive across the range of each population, primarily focussed over continental shelf and slope waters with occasional open ocean excursions.
ISSUES OF IMPORTANCE
The key factor for monitoring status is a lack of information on current population size and trend. Although impact has no doubt been reduced, white sharks are still taken as bycatch in commercial shark fisheries, shark control programs and targeted in response to shark attack/potential hazards. Impacts of shark cage diving operations on white shark physiology is unknown and subject to current research.
DATA STREAM(S) USED IN CASE STUDY
Relevant peer review publications and reports, aerial survey and tagging data.

Tags: Carcharodon carcharias, case study, expert assessment, population status, threatened species, white shark
Organization: Australian Ocean Data Network
Population genetics of the fissiparous Holothurian, Stichopus chloronotus, on the Great Barrier Reef

Population genetic structure was studied in one nearshore (Great Palm Island) and two offshore (Rib Reef and Reef 18-026) populations of Stichopus chloronotus on the Great Barrier Reef. Two stations approximately 500m were sampled on each reef at depths between 1 and 2 m. At each station, 30-40 individuals were sampled within a radius of 30m, in early November 1996. The sampling time in November was chosen to increase the likelihood of finding mature gonads in the sampled animals.Genetic variation at 5 polymorphic loci was examined using allozyme electrophoresis. The polymorphic enzymes examined were: hexokinase (E.C. 2.7.1.1; HK), mannose- 6-phosphate isomerase (E.C. 5.3.1.8; MPI), phosphoglucomutase (E.C. 5.4.2.2; PGM), triose-phosphate isomerase (E.C. 5.3.1.1; ¹PI) and peptidase using valylleucine as substrate (E.C. 3.4.11/13; Estimates of the level of asexual reproduction were made using the ratios of the number of sexually produced individuals to sample size, observed genotypic diversity (Go) to expected genotypic diversity (Ge), and number of genotypes (Ngo) to sample size. Values of Go/Ge much smaller than one indicate the occurrence of clonal reproduction.F-statistics were used to partition genetic variation into that occurring within populations (FIS) and that occurring between populations (FST).
 To study levels of asexual reproduction and genetic variations occurring within and between populations.
 Stichopus chloronotus is a common holothurian species on Indo-Pacific coral reefs.

Organization: Australian Ocean Data Network
Surveys of deepwater benthic communities using a benthic sled in Ningaloo Marine Park, Western Australia (WAMSI Node 3 Project 1 Subproject 3.1.1)

Towed video footage and single beam sonar allowed for the detection and targeting of different benthic communities with the benthic sled, so species and functional groups could be identified and their distribution, abundance, biomass and size composition investigated.50 sites were sampled in 2006 and a further 12 sites were sampled in 2007. Sites were located at various depths in different habitats with varying degrees of benthos.
 Due to the large size of some of the benthos collected (i.e. sponges and gorgonians) in the 2006 field work, the dimensions of the CSIRO designed benthic sled were sometimes inadequate for the purposes of our survey and a new sled was designed and built for the 2007 field work. The new steel benthic sled is based on the design of a commercial fishing Tri-gear Trawl Beam, slightly modified for our purposes. Traditionally a Tri-gear Trawl Beam is used to locate, track and sample scallops and deep water prawns in depths less than 1000 metres. The dimensions of the sled used at Ningaloo are 1.5 m wide x 1 m high. The net and cod end are made of 48 ply 2" Amican TM. It is a 4 seam net; top and bottom panels 100 meshes wide with wing panels 50 meshes high. It has a 9 bar 1 point taper with panels 75 meshes long with dimensions of 55 meshes long and 100 meshes round. The net and cod end are protected by rubber chafe matting designed to minimise damage from abrasive substrates (i.e. rock, coral). There is a double cod end to help secure the sample from being lost from a torn net.Trials indicated the new sled's sampling was an improvement on 2006 and all the macro benthos shown on towed video was being sampled. Trials also indicated that the most representative and manageable sled sample distance, out of several tested, was 50 metres in all the habitats sampled. Fifty metre long samples will be adopted as the standard for future samples to be carried out in 2008.

Organization: Australian Ocean Data Network
Population genetics of squid species in northern Australian waters

A study of the population genetics of squid of the genus Loligo was carried out at 9 northern Australian locations. Variations in gene frequencies of allozymes and common proteins were used to estimate connectivity and dispersal between populations, and to determine the phylogeny of the genus (discrete species identities). Two previously described species (Photololigo chinensis, P. edulis) were discovered to actually be four species.Sampling locations were: Northwest Shelf, Timor Sea, Arafura Sea, Gulf of Carpentaria, Torres Strait, Cape York, Princess Charlotte Bay, Townsville, Brisbane. Sample sizes for the locations ranged between 19 and 447 individuals. Species identified were: Photololigo chinensis, sp.1, sp.2, sp.3.Following preliminary scoring for 76 enzymes, 9 enzymes were selected for routine scoring of genotypes: ACON, AK, ENOL, IDH, MDH-3, MPI, PGDH, PGM, G3PDH.
 To estimate connectivity and dispersal between populations, and to determine the phylogeny of discrete species.

Organization: Australian Ocean Data Network
Developing methods for commercially farming bath sponges in the Palm Island group, central Great Barrier Reef

In August 2005, experimental farming of the sponges Coscinoderma sp. and Rhopaloiedes odorabile commenced at three of the nine islands of the Palm Island group in the central Great Barrier Reef: Great Palm Island (1 site), Fantome Island (3 sites) and Pelorus Island (2 sites).Eleven farming techniques were tested. These were grouped into four general categories: threaded line, cut explant, spike and mesh panel methods. Within each category different materials such as nylon, polyethylene and polypropylene lines or different compartment sizes were trialled.Sponge explants were obtained by partially harvesting approximately 20 sponges of each species from the local populations, keeping the sponges underwater at all times. Both Coscinoderma sp. and Rhopaloiedes odorabile explants were deployed within 2 x 2 m plastic grids, suspended upright 3 m from the substrate at an average depth of 12 m. Three grids were used per sponge species, each holding 5 replicates of each treatment (farming technique). Survival and growth of the explants were monitored in situ every few months over a period of 2 years to determine if there were also seasonal differences.The importance of a nursery period for Coscinoderma sp. and Rhopaloiedes odorabile was examined by comparing growth and survival of explants threaded onto 4 mm nylon line, explants farmed in mesh panels and explants placed in mesh panels for 4 months then threaded onto nylon line. Explants were obtained by partially harvesting approximately 5 individuals of each species. For both species, 5 replicates of each treatment were used. The ropes or mesh strips were &gt;= 1 m apart, in an upright position at a depth of approximately 12m. Each method replicate had 5 explants approximately 15 cm apart. The explants were farmed for a period of 9 months.
 An experiment was carried out to test a range of farming techniques at different locations within the Palm Island group, to determine the most successful method and location for commercially farming Coscinoderma sp. and Rhopaloiedes odorabile. For both species, a second experiment was carried out to determine whether growth and survival using the threaded line technique, was higher in explants, which were first allowed a 'nursery period' during which explants were allowed to heal in mesh panels.

Organization: Australian Ocean Data Network
Surveys of octocorals in the Rowley Shoals Marine Park and the Mermaid Reef National Marine Nature Reserve, Western Australia

Octocoral biodiversity was surveyed at eighteen sites across all three Rowley Shoals (Mermaid, Clerke and Imperieuse Reefs). At each site, transects commenced at ~20m depth and ascended gradually, finishing at ~5m depth over a horizontal distance of ~300m. All octocorals encountered were identified (so far as possible in the field), most were photographed and selected samples were taken of new observations for later taxonomic analysis.The data will be maintained by AIMS, while the WA Museum will hold the taxonomic specimens.
 This research was undertaken as a component of a major biodiversity survey of the Rowley Shoals Marine Park and the Mermaid Reef National Marine Nature Reserve. The survey was undertaken in response to management information needs and was aimed at collecting data that could directly inform management of the Rowley Shoals Marine Park and the Mermaid Reef National Marine Nature Reserve.The octocoral data has been used to produce a basic photo ID guide to facilitate analysis of benthic monitoring video tapes from the Rowley Shoals.
 A subset of the data has been provided to the Ocean Biogeographic Information System (OBIS, http://www.iobis.org/OBISWEB/DisplayMetaData.jsp?content=meta/1460.html).

Organization: Australian Ocean Data Network
The Phytoplankton Ecology of Wilson Inlet, Western Australia - Nutrient Limitation of Phytoplankton Biomass

Nutrient deletion bioassays were applied over a one-year period to the phytoplankton community of Wilson Inlet.  The bioassay data was supplemented with in situ measurements of physical and chemical variables to provide an indication of the nutrient status of the estuary and of the potential for the phytoplankton to become nutrient limited.

Tags: Biosphere | Ecological Dynamics | Bioavailability, Biosphere | Microbiota | Phytoplankton, Oceans | Coastal Processes | Inlets
Organization: Australian Ocean Data Network