AndreaBozzo/ceres-open-data-index huggingface dataset:
Mean grainsize of surface samples collected from the reef flat physiographic zone of Wistari Reef

Wistari Reef is a lagoonal platform reef, situated on the Tropic of Capricorn, within the Capricorn and Bunker region of the southern Great Barrier Reef. Five surface samples were taken from the reef-flats and analysed to determine mean grainsize and the sorting coefficient (expressed as the standard deviation of grainsize). Results indicate that the reef flat area has an average mean grainsize is ~0.19phi, with an average sorting coefficient of 0.58phi.

Tags: Oceans | Coastal Processes | Coral Reefs, Oceans | Marine Sediments | Sediment Grain Size, dominant_coarse_biota, dominant_fine_biota, grainsize, sorting_coefficient
Organization: Australian Ocean Data Network
Western Australia - National Intertidal-Subtidal Benthic NISB Habitat Map (PLUS)

The NISB Habitat Map was created by the University of Tasmania for a partnership between the Department of Climate Change and the National Land and Water Resources Audit. It supports the DCC/Audit partnership by providing a nationally consistent set of the available mapping data for those habitats that occur between the approximate position of the highest astronomical tide mark (HAT) and the location of the outer limit of the photic benthic zone (approximately at the 50-70 m depth contour). This area is broadly equivalent to the 'inner' and 'mid-shelf' regions identified by Geoscience Australia. The resulting map data set forms a core component of the ECM National Habitat Map Series. The habitat classes include: coral reef, rock dominated habitat, sediment dominated habitat, mangroves, saltmarsh, seagrass, macroalgae and filter feeders (e.g. sponges), as defined in the NISB Habitat Classification Scheme. The scheme is designed to support the development of marine 'ecoregions' or bioregional subregions. Details of the scheme and the process of its development are available in National Intertidal/Subtidal Benthic (NISB) Habitat Classification Scheme Version 1 (Mount, Bricher and Newton, 2007). The NISB Habitat Map consists of two layers for each state. _NISB.shp consists of the entire available habitat mapping at a resolution finer than 1:50 000 (with a few exceptions, outlined in the data quality section below). _NISB_PLUS.shp consists of all the data in _NISB.shp along with coarser resolution data, including NVIS and OzEstuaries data. These layers were used to produce the National ECM Key Habitat Distribution Map Series 10 km and 50 km tile maps.
Note: This data is labelled as “NISB_plus”, indicating that it is the NISB Habitat layer plus other lower quality layers.

Tags: Australia, Western Australia
Organization: Australian Ocean Data Network
Natural Hazards: Tropical Cyclones of Australia: predictions and management.

In Australia, tropical cyclones are mostly experienced in north west Australia between Exmouth and Broome in Western Australia and in north east Queensland between Port Douglas and Maryborough. In the Australian region, the official tropical cyclone season runs from 1 November to 30 April with most occurring between December and April. On average, about 10 cyclones develop over Australian waters each year and around six of these cross the coast.
This website explains the cause, characteristics and consequences of Cyclones. Information about, historical cyclones and other natural disasters is also available. 
Featured web pages are :
    *  Emergency Management Australia - Cyclones
    * Bureau of Meteorology - Surviving Cyclones
    * Bureau of Meteorology - El Niño/Southern Oscillation wrap up
    * Bureau of Meteorology - FAQ
    * Bureau of Meteorology - Cyclone Names
    * National Oceanic Atmospheric Administration - Climate Predition Center
    * Australian Severe Weather - Cyclone
    * Emergency Management Australia Library

Tags: Atmosphere | Atmospheric Phenomena | Cyclones, Atmosphere | Atmospheric Pressure | Anticyclones/cyclones
Organization: Australian Ocean Data Network
Development of a genetic method to assess bleaching tolerance in corals (MTSRF Project 2.5i.2c)

Next generation DNA sequencing was used to scan a large proportion of the transcribed coding DNA in Acropora millepora for polymorphisms. Transcribed coding DNA (messenger RNA - mRNA) was extracted from 8 colonies sampled at three thermally distinct habitats along the GBR (Wilke Island Reef in Princess Charlotte Bay, Nelly Bay at Magnetic Island, and Miall Island in the Keppel Islands). The mRNA extractions from each population were pooled and translated back to the complementary DNA (cDNA), which was sequenced using 454 pyrosequencing by the Australian Genome Research Facility. This transcriptome consists of over 500 000 DNA sequences that are assembled into 55 000 contigs, of which over 11 000 aligned to known genes (8 000 unique genes). A database was generated consisting of almost 90 000 SNPs (Single Nucleotide Polymorphisms/gene variants).26 SNPs from 16 genes were investigated, from which one SNP from each of 15 genes were deemed suitable for large scale genotyping and a genotyping assay was developed.20 individuals from 17 reefs throughout the Great Barrier Reef were genotyped. Four from the 15 show a geographic pattern.The relative frequency of each of the nucleotides was measured in each SNP (A, T, C, G).
 To investigate the variation in gene coding regions and their frequency distributions along a themal gradient on the Great Barrier Reef with the aim of using such genes as markers to map thermal tolerance across the Great Barrier Reef.To describe DNA sequences for genes that are likely to be involved in thermal stress responses.To describe gene variants and their potential function in the coral host.To map allele frequencies of these genes at select locations on the GBR.
 Reef locations: Boulton Reef, Calder Island, Darley Reef, Emily, Goble Reef, High Peak Island, Holbourne Island, Night Island, North Keppel, Reef 20-344, Reef 21-121, Ross Reef, Sudbury Reef (I and II), SW Pelorus, Wilkie Island, Wallace Island.15 selected genes: Argenine Kinase, Beta Gamma Crystalin, Coatomer, Complete Component C3, Feritin, Galaxin, Gene of unknown function, Hsp60, Ligand of number X2, Mn Superoxide Dismutase, Thioredoxin, Transcription factor 1_1, Transcription factor 1_5, Ubiquitin like protein.The image is a portayal of one of the gene distributions.

Organization: Australian Ocean Data Network
Water quality monitoring system - Darwin Harbour, Northern Territory

Darwin Harbour is a tropical estuarine system with a distinct wet and dry season and is one of Australia's largest deep water harbours (Russell and Hewitt 2000). The annual rainfall of Darwin averages 1714 mm, with 64% of this falling between January and March. The harbour is macro-tidal, with a maximum tidal range of 7.8 m and strong currents of up to 2 m/s that transport sediment within the harbour. Nine sites were sampled throughout the harbour on a quarterly basis at the neap tides between December 2002 and December 2004. Sites ranged in depth from 5 m (river sites) to 30 m (outer harbour sites). Highly seasonal rainfall in this region greatly affects the water quality throughout Darwin Harbour, with the results from this study showing that seasonal aspects, rather than spatial or tidal, are more important in causing significant differences in water quality. However, while nutrient, suspended solid and chlorophyll a concentrations differed between locations within the harbour, rainfall appears to have the greatest impact on these parameters. Darwin Harbour is a well mixed, though not a well-flushed system, with a huge tidal range that causes large volumes of water to move into and out of the harbour. This in turn leads to considerable differences in water mixing between different areas within the harbour and so one would expect that the concentrations of nutrients, chlorophyll a and suspended solids would be greatly influenced by this. Interestingly, our observations did not detect significant variations during the tidal studies, but did detect significant differences between wet and dry seasons. Darwin Harbour water quality, as observed during this study, was not significantly different to that observed by Padovan (1997) 12 years prior to this study. This is despite the considerable alterations and developments in the harbour and the surrounding catchment during this period.
 This study was undertaken to expand the existing monitoring work in the harbour carried out by the Northern Territory Department of Natural Resources, Environment and The Arts (NRETA) and to provide additional baseline information of water quality.
 Parameters measured: temperature, salinity, turbidity, nutrients, chlorophyll a, particulate nitrogen, particulate phosphorus and suspended solids concentrations.

Organization: Australian Ocean Data Network
Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching, Western Australia

Data on the variation of microsatellite markers and changes in coral cover at 6 sites at Scott Reef were used to identify:1. At which sites were Seriatopora hystrix worst affected by bleaching.2. The scale of genetic subdivision of S. hystrix at Scott Reef 5 years after the bleaching event, and to what extent had the majority of larvae dispersed (metres or tens of kilometres).3. Whether new recruits at the most severely bleached sites were produced locally (from a few remaining colonies), from other sites on the same reef, or from other reefs within the Scott Reef system.All sites consisted of 5 permanent 50 m transects on the reef slope at about 9 m depth. Transects were filmed 6 months before (October 1997), 6 months after (October 1998), and approximately 5 years after (November 2003) a bleaching event which occurred in February 1998. Percentage cover (estimated using a point intercept method) was calculated from the mean percent cover over the 5 transects at each site for each year.In January 2004, 287 samples from individual colonies of S. hystrix were collected from 6 sites within the Scott system: south Scott (SL1, SL2 and SS1), north Scott (SL4), Sandy Islet Reef (SL5), and Seringapatam Reef (SS3). At each site, the exact location of each sampled colony along a permanent 300 m transect was recorded, along with the global positioning system coordinates at the beginning of each transect. Between 45 and 50 colonies were sampled at regular intervals along each transect.Genotyping of the 287 individuals was carried out. Because only two pairs of individuals shared the same diploid multilocus genotype, one individual from each of these pairs was removed from subsequent analyses so that each unique genotype was represented only once.Characteristics of the 9 Seriatopora hystrix microsatellite markers recorded were: the number of unique multilocus genotypes (N), the number of alleles (A), the proportion of observed (HO) and expected (HE) heterozygotes per locus and site, and the FIS calculated for each locus and each site (FIS All). Loci: Sh2-002, Sh2-006, Sh4-001, Sh4-010, Sh3-003, Sh3-004, Sh3-007, Sh3-008, Sh3-009, Sh4-001, Sh4-010. Allelic frequencies, allelic patterns and expected heterozygosities under Hardy-Weinberg equilibrium, and the number of private alleles were calculated in Genalex v6.Tests for Hardy-Weinberg and linkage disequilibrium were conducted using FSTATv2.9.3a spatial autocorrelation analysis, applied within each site.
 To explore the fine-scale processes influencing the local genetic structure and assess present day migration patterns over larger scales for S. hystrix at the Scott Reef system using high resolution genetic markers in combination with a detailed sampling design.To explore the influence of larval dispersal and adult abundances on rates of recruitment and recovery of this species following a catastrophic disturbance (bleaching) in an isolated system.

Organization: Australian Ocean Data Network
Theme 3D: Development of new methodologies for measurement of restoration.

Deterioration of coastal marine and estuarine habitats is inevitable in areas where human development is active. This is particularly the case in New South Wales (and throughout Australia) where a very large proportion of the population live on the edges of the coast-line. To sustain biodiversity and to maintain ecological processes and functions (for its own sake or for anthropocentric, human reasons), it will be necessary, for a very long time, to recreate, rebuild or repair habitats (Programme 3: Restoration of Disturbed Coastal Habitats). The science of restoration of coastal habitats is virtually unknown, and there is no sensible theory or understanding of how to create habitat that develops ecological function and maintains natural biodiversity. 
Most projects on restoration of habitat have unclear or no defined aims. Where there are clear aims, it is unusual, if not rare, to find any assessment of whether the aims are being achieved. The Centre for Research on Ecological Impacts of Coastal Cities (EICC)'s research in the area of ecology includes development and testing of protocols to allow assessment of the progress and achievements of programmes of restoration. This is complex because, like assessments of impacts, any actual restoration must be detectable against large natural variation in numbers and types of animals and plants from place to place and time to time. Also, the goals of restoration cannot depend on vague hopes of "restoring a balance" when it is known there is no "balance" to restore. So, sampling and experimental design, logical structures for statistical analysis and interpretation of results must all be developed, tested and improved. 
The EICC has generated many scientific papers and theses from research projects on the development and testing of protocols to allow assessment of the progress and achievements of programs of restoration. The link to the URL provided in this record provides a link to this research.

Tags: Coastal Habitats, Ecology, Oceans | Marine Biology | Marine Habitat, methodologies, restoration
Organization: Australian Ocean Data Network
IMOS - Ocean Radar - Green Head HF ocean radar station (Turquoise Coast, Western Australia, Australia)

The Green Head (GHED) HF ocean radar site (30.073 S 114.967E) is one of two HF ocean radars covering Rottnest Shelf and Perth Canyon on the Turquoise Coast north of Perth.  The other HF ocean radar station is at Seabird, or Lancelin from 2013-03-19.  The HF ocean radar coverage is from the coast to beyond the edge of the continental shelf. 
The GHED HF ocean radar is a SeaSonde crossed-loop direction finding array.  This radar operates at a frequency of 5.211 MHz, with a bandwidth of 50 KHz, a maximum range of 200 Km and a range resolution of 3 Km.  The antenna bearing is 288 deg true east of north (approximately west by north-west).
Within the HF radar coverage area surface current radials are measured.

Tags: Coastal Cities / Towns (Australia) | Perth, WA, Doppler Frequency, Global / Oceans | Indian Ocean, Marine Features (Australia) | Perth Canyon, WA, Oceans | Coastal Processes | Coral Reefs, Oceans | Ocean Circulation | Eddies, Oceans | Ocean Circulation | Ocean Currents, Oceans | Ocean Circulation | Upwelling, Oceans | Ocean Circulation | Wind-driven Circulation, Physical Oceanography, Radiance Or Imagery | Radio Wave | Radio Wave, SeaSonde (CODAR) HF Radar | Amplitude Direction Finding, States, Territories (Australia) | Western Australia
Organization: Australian Ocean Data Network
Floristic analysis of vegetation site data from the Burrup Peninsula, Dolphin, Angel and Gidley Islands with data from Cape Preston the Chichester Range

Former Department of Resources Development commissioned a vegetation survey of the Burrup Peninsula to improve knowledge of flora and vegetation communities.
Flora, vegetation and floristic survey for the assessment of the conservation values, including placing the vegetation and flora in a wider context by comparing floristics with areas on the adjoining mainland.
Survey methodology, duration etc is given in Volume 1.

Tags: Biosphere | Vegetation | Vegetation Species, Conservation, Flora, Habitat, Marine Features (Australia) | Burrup Peninsula, WA
Organization: Australian Ocean Data Network
Ecological Intelligence for Reef Restoration and Adaptation Project (EcoRRAP)

The Reef Restoration and Adaptation Program (RRAP) is a collaboration of Australia&rsquo;s leading experts to create a suite of innovative and targeted measures to help preserve and restore the coral reefs globally. These interventions must have strong potential for positive impact, be socially- and culturally-acceptable, ecologically-sound, ethical and financially-responsible. They would be implemented if, when and where it is decided action is needed &ndash; and only after rigorous assessment and testing. 
The Ecological intelligence for RRAP sub-program is a cross-cutting program that conducts ecological research to boost the success of RRAP interventions by advising on the what, where and when of interventions, and filling crucial gaps in ecological knowledge for the GBR. EcoRRAP&rsquo;s objectives are: 
(1) Provide location-specific knowledge on natural processes for reef recovery without human interventions, and their limitations. 
(2) Deliver knowledge about the natural processes and&iquest;speed of adaptation to a changing environment. 
In 2021 EcoRRAP has established 352 permanent plots (6 x 12 m) on 64 reference reef sites, which span from the Torres Straits to the Southern end of the GBR, and from inshore to offshore reefs, including reef slopes and reef lagoons, across gradients of wave exposure and depth. At the Reference Reefs, critical environmental, genetic, population demographic and community data were collected using traditional and cutting-edge tools including 3D-photogrammetry.  All sites are visited and surveyed annually, and if massive bleaching events occur further surveys may occur, as one of EcoRRAP&rsquo;s research interests is to improve our understanding of coral reef adaptation and recovery potential from acute disturbances, especially those driven by climate change.
EcoRRAP data in their entirety will inform RRAP about site-specific limitations in reef recovery in a wide range of reef habitats represented in the GBR. Traditional Owner consent and GBRMPA permits have been obtained to work at all sites. This is the parent EcoRRAP repository, for details on how each dataset was collected, analysed and interpreted please see the specific repositories for each dataset.

Organization: Australian Ocean Data Network
Trail cameras and boat ramp interviews for assessing perceptions, understandings and recreational fishing of AMPs

Trail cameras were used to collect novel primary data relating to boat ramp use and distributions in relation to an offshore Marine Park (Freycinet Marine Park). Interviews were also conducted on boat ramps of marine recreational trailer-boat fishers to investigate their behaviour and perceptions of FMP.
This record describes the context of the study and methodology. Raw data obtained from trail cameras are attached to this record, all other data is synthesised in the report linked in the 'Online Resources' section.

Tags: Marine and Estuarine Ecology (incl. Marine Ichthyology), National Environmental Science Program (NESP) Marine Biodiversity Hub, Natural Resource Management, behaviours and perceptions, boat ramp monitoring, fishing effort, recreational fishing
Organization: Australian Ocean Data Network
The Australian Phytoplankton Database (1844 - ongoing) - abundance and biovolume

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate over 3,600,000 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://imos.aodn.org.au/), allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels. There is a static snapshot of the database as at March 2016 (http://dx.doi.org/10.4225/69/56454b2ba2f79), and this has been documented in a Scientific Data Publication. This metadata record provides access to the dynamic (most recent) version of the database and was based on the following CSIRO metadata record: https://marlin.csiro.au/geonetwork/srv/eng/search?uuid=1836cea6-317d-1608-e053-08114f8c81ba.

Tags: Continents | Antarctica, Countries | Australia, Countries | Indonesia, Countries | New Caledonia, Countries | New Zealand, Countries | Papua New Guinea, Countries | Solomon Islands, Countries | Timor-Leste, Countries | Vanuatu, Global / Oceans | Indian Ocean, Global / Oceans | Pacific Ocean, Global / Oceans | Southern Ocean, Marine Features (Australia) | Bass Strait, TAS/VIC, Marine Features (Australia) | Great Australian Bight, SA/WA, Marine Features (Australia) | Great Barrier Reef, QLD, Offshore Islands (Australia) | Macquarie Island, Regional Seas | Arafura Sea, Regional Seas | Coral Sea, Regional Seas | Solomon Sea, Regional Seas | Tasman Sea, Regional Seas | Timor Sea, States, Territories (Australia) | New South Wales, States, Territories (Australia) | Northern Territory, States, Territories (Australia) | Queensland, States, Territories (Australia) | South Australia, States, Territories (Australia) | Tasmania, States, Territories (Australia) | Victoria, States, Territories (Australia) | Western Australia
Organization: Australian Ocean Data Network
Australian Coral reef distribution (V7.0, 2003) as subsetted from Global distribution of Coral reefs

The data source of this Australian Coral reef distribution subset  has been compiled by UNEP-WCMC to show the global distribution of warm water coral reefs. This dataset has been created  from multiple sources and is derived from data used in the creation of the World Atlas of Coral Reefs (2001). This polygon feature dataset is an update of the data used in the Atlas but is based on a 1km raster version of the dataset to enable distribution of the data. 
This is due to restrictions placed by some data sources and suppliers.

Tags: Australia
Organization: Australian Ocean Data Network
Marine mammal interactions with trawl gear

Underwater video technology was used to observe marine mammal interactions (seals, in particular Australian fur seals) within midwater trawl nets.
A camera system was placed inside the trawl net in the vicinity of a Seal Excluder Device, designed to prevent megafauna from entering the codend of the net and provide an escape point.
Digital video data was described according to a range of operational, catch and interaction fields, and made time-specific to each trawl shot.  Data is linked to commercial catch and effort data providing operational, environmental and catch information.

Tags: 41 131003, Agriculture | Agricultural Aquatic Sciences | Fisheries, Arctocephalus pusillus doriferus, Oceans | Marine Biology | Marine Mammals
Organization: Australian Ocean Data Network