AndreaBozzo/ceres-open-data-index huggingface dataset:
AIMS Long-term Monitoring Program: Visual Census Fish Data (Great Barrier Reef)

70 selected reefs throughout the Great Barrier Reef (GBR) are sampled in the AIMS Long-term Monitoring Project (LTMP). Underwater visual census is used to survey reef fishes on fixed transects (3 sites per reef, 5 x 50 m transects per site). The abundance and length of all diurnally active, non-cryptic fishes are recorded. A full list of species observed each year can be obtained on request.
The overarching goal of LTMP fish surveys are to detect changes in reef fish communities over time at a regional scale, but also to examine the effectiveness of Marine Protected Areas.
All fish species counted are largely non-cryptic, easily identified underwater and include both commercial and non-commercial taxa. Because surveys span the annual recruitment season, 0+ individuals are excluded from counts: these are distinguished from adults by their small size and often distinctive colouration.
Abundance data for each fish species is subsequently summed over the five transects at each site on each reef to provide reasonable sample sizes for analysis and interpretation.
Updated results of surveys can be found at:
https://apps.aims.gov.au/reef-monitoring/reefs
A subset of the data has been provided to the Ocean Biogeographic Information System (OBIS, http://www.iobis.org/explore/#/dataset/3936).
Data have been used for the e-Atlas:
http://eatlas.org.au/data/uuid/05bde62a-70ec-407b-b999-30cf369498af

Organization: Australian Ocean Data Network
AIMS Long-term Monitoring Program Water Quality Data 1990-1996 (Great Barrier Reef)

Water Quality Data from the AIMS Long Term Monitoring Program. Water and sediments (another dataset) were sampled at the same sites adjacent to all 52 reefs where fish and benthic transects are conducted. Sampling occurs in open water within 500 metres of the reef, on both sides (north and south flanks) of the reef. Sampled reefs occur throughout the Great Barrier Reef, and the reefs of the North West coast of Australia.
 To track change.
 Data recorded includes temperature, salinity, Secchi depth, suspended solids, silicates, ammonium, nitrite, dissolved nitrogen (organic, inorganic and total), dissolved phosphorus (organic, inorganic and total), chlorophyll-a and phaetophytin pigments. Observations commenced in August 1990 and ceased in 1996.

Organization: Australian Ocean Data Network
AIMS Long-term Monitoring Program: Video and Photo Transects (Great Barrier Reef)

Benthic organisms were surveyed annually on fixed sites in one habitat on each of 47 selected core survey reefs from 1993 to 2005 in 6 regions throughout the Great Barrier Reef (GBR). Surveys were undertaken at 3 sites per reef, with 5x50m transects surveyed per site.In 2004 a new zoning plan was implemented in the Great Barrier reef Marine Park and in 2006 the pattern of surveys was changed. The original set of reefs (47) are surveyed in odd years (e.g. 2007) and a different set (56 reefs) are surveyed in even years. The new set consists of paired reefs (one no-take, and one open to fishing) surveyed to assess the effects of rezoning. The paired reefs are near Cairns and Innisfail, Townsville, Mackay, the Swain Reefs and the Capricorn-Brunker group.From 1993 to 2006 video transects were recorded and sub-sampled at 200 points per sample. The program was modified in 2007 to allow collection of data from single frames shot at 1m intervals along each transect using a digital still camera.Benthic groups recorded are: Abiotic; Hard coral; Soft coral; Coralline algae; Macro algae; Turf algae; Sponge; Other; Indeterminate.
 To annually monitor the cover of benthic organisms, reef fish abundance and crown-of-thorns starfish populations on various reefs of the Great Barrier Reef.The program has been designed to track changes in reef communities over time across sub-regions of the GBR.
 Parameters: Percentage cover of different substrate types and benthic organisms (particularly corals), identified to benthic group or lifeform level. Data on reef fish abundance and diversity are collected at the same sites and times.

Organization: Australian Ocean Data Network
Mackay Whitsunday Isaac Healthy Rivers to Reef Partnership Southern Inshore Coral Monitoring Program

Annual Benthic monitoring of six reefs within Southern Inshore Reporting Zone for the Mackay Whitsunday Isaac Regional Report Card
Data utilise the same sampling methods as the Marine Monitoring Program: Photopoint  intercept for benthic cover, counts of juvenile corals in belt transects and scuba searchs in belt transects for vectors of coral mortality.
The methods used are identical to those used by the Marine Monitoring Program as described in                                                                             https://tsv-apps.aims.gov.au/metadata/view/c30cfb2d-46be-4837-9733-9bb60489b65b
At each Pine Peak Island, Pine Islets, Connor Island and Henderson Island, five 20m long transects are monitored at each of two sites and at 2m and 5m depth below lowest astronomic tide. At Aquila Island and Temple Island transects are at 1 to 2m depth only.
Note: Monitoring of Connor Island ceased in 2021 due to visibility and logistic constraints.

Organization: Australian Ocean Data Network
Corals of the World online

Corals of the World online is an interactive program, which captures global information about corals and makes it readily accessible to conservationists, educators and research scientists alike. The program is divided into two linked components, Coral ID and Coral Geographic.
Coral ID is founded on the three-volume book, &quot;Corals of the World&quot; (Veron, 2000) and incorporates updated and expanded species data from the electronic publication &quot;Coral ID&quot; (Veron and Stafford-Smith, 2002). The sophisticated electronic key in this program makes coral identification easy. Species pages give summaries of key characteristics as well as taxonomic detail.
The Coral ID program includes:


A sophisticated (Lucid-based) key taking users directly to species pages. (coming soon)


Species pages containing:
-A character summary
-Underwater in situ photographs
-Photographs of skeletons
-Data on colour, similar species, habitats and abundance
-Detailed account of skeletal and live coral characteristics (coming soon)
-A map showing global distribution from Coral Geographic
-Reference information
-Links to other identification products


A link to Coral Geographic.


Coral Geographic has not been previously published although it has been providing geographic data about corals since the early 1990s. Geographic information can be obtained in a many formats allowing analyses and interfacing with other programs and datasets. The program divides the world&#39;s coral regions into 141 named ecoregions. Features of Coral Geographic will be released progressively over the next few years and will be available (a) interactively on the internet, (b) for downloading in available formats and (c) on DVD.
The Coral Geographic program includes:


For each coral species:
-A GIS map showing global distribution
-Types of presence/absence records available
-Comprehensive references
-A link to the relevant species page in Coral ID


For each ecoregion:
-A comprehensive list of species
-Geographic information and photographs
-Links to other information sources


Multiple species maps which can be selected according to user needs.


Species maps which can be interfaced with other programs according to user needs.


Additional information is available in the form of explanatory chapters about coral classification, coral structure and growth, coral taxonomy, coral environments, reefs, mass bleaching, coral reproduction and coral evolution.
Also, a space where users can insert information for personal use and a link where information and photographs can be submitted for inclusion in program updates is included. (coming soon)
This program has been developed to provide global information about corals to conservationists, educators and research scientists alike.
Early taxonomic classifications were published by J.E.N Veron and Michael Pichon in &#39;Scleractinia of Eastern Australia&#39; Monograph Series, Vol I-V. These publications have been digitised by Atlas of Living Australia, and made available on the Ocean Biogeographic Information System.

Organization: Australian Ocean Data Network
Macrozooplankton from the southern North West shelf, Western Australia

The distribution and abundance of macrozooplankton on the southern North West Shelf of Western Australia was investigated over two consecutive summers (October to February) of 1997-1998 and 1998-1999, using submersible light traps. Sampling was conducted over a period of 10 days centred on successive new moons. Traps were deployed at the surface and at depth along one cross-shelf transect in the first summer, and along two cross-shelf transects and one long-shore transect in the second summer.At each station, a CTD equipped with a fluorometer was deployed within a few metres of the bottom concurrently with light trap sampling. Wind speed and wind direction were obtained from the weather station at Milyering.On retrieval, catches were immediately preserved in ethanol. In the laboratory, one sample of catches from each of the paired light traps was sorted into 14 broad taxonomic groups, distinguished with the unaided eye and counted.Vertical zooplankton hauls were to a maximum depth of 60m using a 0.5 m, WP-2 net of 73 µm mesh fitted with a flowmeter. Samples were filtered through a mesh dish and frozen.
 This research was undertaken to describe the temporal and spatial distribution of macrozooplankton on the North West shelf, using submersible light traps. The relationship between observed distributions and environmental parameters was also investigated. The euphausiids, which are difficult to capture by other means were chosen for more detailed examination.

Organization: Australian Ocean Data Network
Close-range underwater photogrammetry for coral reef ecology: a systematic literature review

125 publications on coral reef photogrammetry were systematically reviewed to assess: 1) its global trends and use; 2) how benthic community data is extracted from imagery; 3) the range of metrics derived and their ecological applications; and 4) key limitations of the approach.
55 metrics derived from photogrammetry, grouped in 10 categories, have been used to inform ecological studies on benthic assemblage, habitat structural complexity, and ecosystem condition and trajectory

Organization: Australian Ocean Data Network
Natural adaptation and assisted evolution of corals to heat stress

In the last 30 years, more than 2,000 research papers have been published on the impact of temperature stress on coral reef organisms. We conducted a review of the literature to objectively examine what is known about the potential for natural adaptation of corals to increased temperatures and the effect sizes of assisted evolution efforts that have been documented to date. To identify relevant studies, we conducted a literature search (January 1st, 1975&ndash;October 27, 2022) using the ISI Web Of Science database and search engine with the following strings to identify relevant peer-reviewed publications: Title = coral, Topic = bleach AND adapt, heat AND adapt, temperature AND adapt, acclimat AND adapt, acclimat AND bleach, acclimat* AND temperature, temperature AND bleach, assisted AND evolution, assist AND gene AND flow, assisted AND migration, gene AND edit, selective AND breed. The initial search returned 2,397 papers that met the above criteria. These papers were examined to assess if the study included the following elements: (1) a heat stress condition under laboratory or field conditions; (2) samples from any life history stage of a coral holobiont (excluding host-tissue extractions that were cultured in the lab, separated from the exoskeleton, or papers based solely on cultures of isolated symbionts or microbes and ignoring the coral holobiont); and (3) data reported for at least one coral species in the order Scleractinia from a tropical environment. A total of 562 publications included all three elements. In some instances, multiple publications were found to report different aspects of the same heat stress experiment, but these were treated as independent experiments given that there was no duplication of data.
Included in this collection is the R code for mapping products presented in the publication, which built on the source dataset Marine Ecoregions Of the World (MEOW).
There is also a document were we present exploratory figures to help readers visualize the potential applications of this dataset.

Organization: Australian Ocean Data Network
Rapid regeneration of Acropora millepora coral recruits after physical damage to the primary polyp

During October and November in years 2017 &ndash; 2019, approx.. 10 gravid adult colonies of Acropora millepora and A. tenuis were collected from 5 to 8 m depth from two inshore reefs of the central Great Barrier Reef. Colonies were transferred from Falcon and Magnetic Island reefs to the National Sea Simulator (SeaSim) to undergo spawning.
Three experiments were conducted on A. millepora recruits at three different stages of early development (1, 3, and 5 d post settlement) to examine the level and type of effects physical damage had on recruit survivorship, growth, and the ability to uptake symbionts after 21 d post settlement.
Larvae (n = 20/well) of 13 d age were added to 10 mL of filtered seawater (0.5 &mu;m) in 6-well culture plates (n = 56 wells), each well containing three crustose coralline algae (CCA) chips (4 &times; 4 mm) of P. onkodes in the centre of the well. CCA chips were only used to induce settlement and after ~20 h were removed, and settlement was assessed. The settled recruits were 0.7&ndash;0.9 mm in diameter.
Damage types included:
            a) Recruits were sliced once with a scalpel at a haphazard distance between the mouth (centre) and the edge of the recruit, resulting in a mean incision 20&amp;ndash;30 &amp;mu;m thick. to create various levels of damage

b) Sections of the recruit were removed using a scalpel to create various levels of damage
Recruits were imaged at four time-points: before tissue damage, immediately after tissue damage, 1 day after tissue damage and 21 days after tissue damage (i.e., 3-weeks after settlement) using a Leica stereomicroscope fitted with a 14-MP microscope camera (CMOS C-Mount) shot at 1.25 &times; optical zoom.
Recruits were considered alive if tissue covered the basal plate. Survivorship, horizontal growth and surface area analysis were conducted to examine the post-settlement survivorship

Organization: Australian Ocean Data Network
Tide gauge deployment, Middle Island, southern Great Barrier Reef (SGBR Project 1989-1990)

An Aanderaa WLR was deployed at Middle Island (Station MD1).Deployment Details: Date deployed: 31/8/89 (SGBR1) Date recovered: 27/2/90 (SGBR3)Instrument: WLR #869Depth: 5mSampling regime: 41 sec integration time at 30 min intervals
 This deployment was a component of the SGBR Project 1989-1990.

Organization: Australian Ocean Data Network
Chemical and biological oceanographic surveys of the Gulf of Papua and Torres Strait (1979)

An oceanographic survey of the Gulf of Papua and Torres Strait was undertaken in November and early December 1979, prior to the monsoon season. In the Gulf of Papua, sampling positions were selected to measure the diffusion of river water into the Gulf. An additional transect was made through the Great Barrier Reef Lagoon (from the Coral Sea to slightly west of Torres Strait) in a preliminary examination of zooplankton production. This dataset contains temperature, salinity, dissolved oxygen, dissolved inorganic and organic nutrient, chlorophyll and phaeophytin data from a range of depths at the 45 stations sampled during this survey. Zooplankton abundance data is also available for 12 stations.Comparisons of AIMS and CSIRO sampling and analytical methods were also made at an intercalibration station in the Coral Sea off Raine Entrance.
 The Gulf of Papua is bordered by a coastline of very high productivity with extensive mangrove forests, and is the catchment area for massive freshwater runoff from the Fly, Turama, Aird and Purari River systems. The adjoining Torres Strait forms a potential pathway for transport of waters between the Arafura Sea and the Coral Sea. The effects of water circulation in this region on the reef ecosystems is of considerable scientific interest.
 A number of additional studies of currents and water movements were also undertaken simultaneously with this cruise, within these waters and the northern region of the Great Barrier Reef. Measurements of the discharge of streams flowing into the Gulf of Papua were programmed by the Office of Minerals and Energy of Papua New Guinea. A CSIRO buoy was also released from RV Lady Basten in the Gulf of Papua during this period and tracked by satellite. The Coastal Zone Colour Scanner on board NOAA satellite Nimbus-7 was programmed for operation over the northern Great Barrier Reef during the cruise. Moored current meters and water level recorders were also deployed by AIMS for several weeks in this period at various locations in the northern region of the Great Barrier Reef. Towards the conclusion of this cruise, geophysical tows were made by the Australian Department of Mineral Resources in the Great Barrier Reef lagoon, south of 11°S. The AIMS components of these additional studies are described separately.

Organization: Australian Ocean Data Network
Manly Hydraulics Laboratory Waverider buoys - Sea surface temperature data

Manly Hydraulics Laboratory (MHL) (part of the NSW Department of Planning, Industry and Environment (DPIE), which has assumed function of former NSW Office of Environment and Heritage (OEH)) operates a system of Waverider buoys off the NSW coastline. The buoys measure wave height and other wave statistics such as wave period on a continuous real-time basis, and are also capable of measuring wave direction (wave data accessible via related metadata record: Waverider buoys Observations - Australia - delayed (National Wave Archive) - https://catalogue-imos.aodn.org.au:443/geonetwork/srv/api/records/2807f3aa-4db0-4924-b64b-354ae8c10b58) and sea surface temperature (SST). The data is gathered by the Waverider system developed by the Dutch company, Datawell, namely thermistors that are mounted inside the hull of the buoys, at the base of the buoy about 0.5m below the water surface. The SST data is stored on the receiving station PC before routine transfer to Manly Hydraulics Laboratory via email.

Tags: Coastal Cities / Towns (Australia) | Byron Bay, NSW, Coastal Cities / Towns (Australia) | Sydney, NSW, Countries | Australia, Global / Oceans | Pacific Ocean, Marine Features (Australia) | Batemans Bay, NSW, Oceans | Ocean Temperature | Sea Surface Temperature, Regional Seas | Tasman Sea, States, Territories (Australia) | New South Wales
Organization: Australian Ocean Data Network
Patterns in the chaos: scale and the spatio-temporal dynamics of GBR reef fish assemblages

This paper analyses the spatial patterns and temporal dynamics of the long-term fish dataset from the LTMP (see LTMP metadata for details on methods).
The dataset spand 233 coral reef fish species, recorded from 1995 to 2023 across the entire GBR.
We analysed spatial patterns and temporal dynamics at the whole GBR scale and the sector x shelf scale, by year and decade, and by total density and species richness, family level and species level. We used Bayesian  glmms, and multivariate techniques such as PCA, Adonis and RDA.

Organization: Australian Ocean Data Network
Ingestion and Depuration of Microplastics by a Planktivorous Coral Reef Fish, Pomacentrus amboinensis

This published research assesses microplastic ingestion and retention by coral reef fish, which are important information to assess ecological risks of this emergent contaminant to the Great Barrier Reef (GBR, Australia). Fish were collected with SCUBA and nets at Lizard Island (North GBR), exposed to microplastics under laboratory conditions at Lizard Island Research Station, and processed (i.e., gastrointestinal tract chemically digested, filtered and analysed under microscope) to assess microplastic ingestion at the Australian Institute of Marine Science (AIMS) in Townsville (Queensland, Australia). Data was statistically analysed using general linear model in R, kinetics model, one-way ANOVA and Tukey&rsquo;s multiple comparisons tests.

Organization: Australian Ocean Data Network
Townsville Bicycle Counts

Bicycle Network’s ‘Super Counts’ programs count the volumes of bicycles and other active travellers, and their movements on roads and paths. Road users are counted visually by volunteers.

This dataset is an extract of the Bicycle Network Super Counts Data Dashboard 2024, specifically the Bicycle Network Commuter Volume Data, for the Townsville Local Government area.

Although all due care has been taken to ensure that this data is correct, no warranty is expressed or implied by Townsville City Council in its use.


Tags: bicycle, bicycle count, bicycle volume
Organization: Townsville City Council
Using Marine Turtles to Identify Habitat and Assess Connectivity of the North and North-West Marine Park Networks and Sea Country

This project compiled marine turtle satellite tracking data for four species: green (Chelonia mydas, n=126), flatback (Natator depressus, n=164), hawksbill (Eretmochelys imbricata, n=59) and olive ridley (Lepidochelys olivacea, n=27) turtles, as well as a comprehensive dataset of modelled benthic habitat data from Northern Australia. Tracking data were used to build species-level movement network models to identify connectivity among Australian Marine Parks (AMPs), Indigenous Protected Areas (IPAs) and State Marine Protected Areas (MPAs) across the North and North-West Marine Regions. Tracking datasets were further processed to classify foraging behaviour and quantify foraging activity spaces. Foraging activity spaces were then overlayed with existing modelled benthic habitats using local entropy analysis to assess how well turtle foraging spaces can be used to identify benthic habitats.

Organization: Australian Ocean Data Network
NESP MBH A5 - Defining the connectivity of Australia's hammerhead sharks

Reports and factsheets associated with the NESP Marine Biodiversity Hub A5 project - Defining the connectivity of Australia&#39;s hammerhead sharks
https://www.nespmarine.edu.au/project/project-a5-defining-connectivity-australia&rsquo;s-hammerhead-sharks

Organization: Australian Ocean Data Network
NWSSRP Theme 1 - Marine Noise Monitoring and Impacts

Investigate selected potential impacts of exposure to a seismic survey on demersal fishes, pearl oysters and infauna across different spatial and temporal scales. Man-made noise is increasing rapidly in marine environments and is recognised as a pollutant of global importance. Management of this issue requires a better understanding of the effect of noise on organisms at all levels of the marine food chain.
As part of the North West Shoals to Shore program, AIMS is investigating the long and short-term impacts of marine noise from the petroleum industry on plankton, pearl oysters and fish.
The studies are also measuring the quality and amount of noise pollution produced by the seismic surveys and vessel activity to produce real-world information about the impacts.

Organization: Australian Ocean Data Network