AndreaBozzo/ceres-open-data-index huggingface dataset:
Investigations into the use of benthic foraminifera as indicators for water quality on the Great Barrier Reef (MTSRF Project 3.7.1)

Sediment samples for foraminiferan community analysis were collected from 20 reefs located between 13.5°S and 20.5°S within the Great Barrier Reef. Most of these reefs are inshore fringing reefs which can be grouped into three distinct geographical regions: eight reefs of the Whitsunday area (collected in August 2004), four reefs from Princess Charlotte Bay, and four from the Wet Tropic area (both collected in October 2004). Sediments were also collected from two midshelf reefs (Charity and Bait Reefs) in August 2004, and two outer shelf reefs (Hastings and Flynn Reefs) in January 2005.On each reef one location of the sheltered back reef and one on the more exposed front reef was chosen. At each location, two samples of &gt; 50 g sediment were carefully scraped from the top 0.5 - 1 cm at 7 to 9 m depth. Samples were fixed in 100% ethanol.To determine sediment chemistry and granulometry parameters, additional sediment samples were collected at the same sites during collection of the foraminifera. In the Whitsunday area, additional sediment samples were collected in August 2005 and February 2006. The sediment samples were taken in triplicate from each location using mini-corers (cut-off 60 ml syringes); only the top 1 cm of sediment was used.Surveys in the Whitsunday region of the GBR included a more detailed study of foraminifera along an inshore-offshore transect.
 Benthic foraminifera are established indicators for coral reef water quality conditions in Florida and the Caribbean Sea. The goal of this research was to contribute knowledge of the ecology of benthic coral reef foraminifera needed to test if these protozoans can be used as indicators for water quality on the GBR and potentially other reef systems in the Pacific region.
 Reefs Surveyed1. Princess Charlotte Bay: McDonald Reef, Hay Island, Wilkie Island, Hannah Island 2. Wet Tropics: Fitzroy Island, High Island, Russel Island, Dunk Island3. Mid/Outer Shelf Reefs: Hastings Reef, Flynn Reef, Charity Reef, Bait Reef 4. Whitsunday Islands: Deloraine Island, Border Island, Whitsunday Island, Hook Island, Dent Island, Island, Lindeman Island, Repulse IslandOther datasets relate to this project, see separate metadata records.

Organization: Australian Ocean Data Network
WAMSI 2 - Kimberley Node - Project 2.2.6 - Terrestrial-Ocean Linkages - Pawsey

This project aimed to understand how dissolved and particulate material from freshwater systems in the Kimberley are transported by the tides and currents into the coastal marine environment and whether these exports from land play a role in coastal productivity. The project linked closely with WAMSI 2 KMRP projects 2.2.1 and 2.2.2 to better understand how freshwater discharge influences marine food web structure and sustains the productivity of Kimberley inshore ecosystems. Oceanographic and biogeochemical data was collected over two field campaigns (October/November 2013 and April/May 2014) from the Walcott Inlet, Collier Bay area (16° 22.624’S 124° 26.235’E to 16° 24.487’S 124° 54.035’E) and models integrated with those for Collier Bay (KMRP Project 2.2.2).
This metadata relates to UWA component of study.  Related CSIRO metadata is located here -
 http://www.marlin.csiro.au/geonetwork/srv/eng/search#!fc8bbadc-3242-06db-e043-08114f8c34f5
Data stored at Pawsey.  CTD_casts_Mar2014, CTD_casts_Oct2013, Hydrology_model_outputs (Walcott_xx.xlsx), Bathymetric_data.csv, ADCP_Jun2014.mat, ADCP_Oct2013.mat, Water_samples.xlsx, SBE39.xlsx

Tags: Biosphere | Ecological Dynamics | Primary Production, CTD (Conductivity-Temperature-Depth Profilers), Concentration of chlorophyll per unit volume of the water body, Concentration of oxygen {O2} per unit volume of the water body, Current Meters/Profilers, Current direction in the water body, Depth, Downwelling vector irradiance as photons (PAR wavelengths) in the water body, Nutrients, Temperature, Tide Gauges, Turbidity of the water body
Organization: Australian Ocean Data Network
Sediment trap data sets for sites around Cleveland Bay - 1993

This metadata record covers a subset of the data collected during dredging by the Townsville Port Authority in Cleveland Bay in 1993.   Data are divided into a number of main groups: Wind, tide gauge, wave rider, S4, sediment traps, water samples and nephelometers.  The data are grouped according to collection method and sampling location. See the metadata record title for collection method and geographic extent for the sampling location. Unique site numbers were assigned within Cleveland Bay at which data were collected.  Some of these sites were named, and others were unnamed.

Tags: Oceans | Marine Sediments | Sedimentation, Sediment traps
Organization: Australian Ocean Data Network
Future Reef MAP - October 2013 (Northbound)

Data were collected as part of the FutureReef MAP project, a three-year project designed to monitor ocean chemistry along the entire length of the Great Barrier Reef. The Future Reef MAP project is funded by Rio Tinto Alcan and administered by the Great Barrier Reef Foundation, with an equal co-investment by CSIRO. The project is the first large-scale CO2 observing system established on the Great Barrier Reef using the Rio Tinto ship, RTM Wakmatha. The research is targeted at providing information on the CO2 uptake and the controls on ocean acidification change in the region. It is providing foundation data needed to assess the vulnerability of the GBR reefs to ocean acidification. This dataset contains quality controlled underway measurements of the fugacity of CO2, atmospheric pressure, and sea surface temperature and salinity. The data management and distribution of these data were supported by the CSIRO Carbon Collaboration Cluster and the Australian Coastal Ecosystem Facility.

Organization: Australian Ocean Data Network
WAMSI Node 3.2.2c - Spatial variation in algal-herbivore interactions on the Ningaloo Reef, Western Australia

This study was nested in sub-project 3.2.2 “Ecosystem impacts of human usage and the effectiveness of zoning for the biodiversity conservation” in Node 3.2. The focus of this study was on trophic effects in the NMP. Due to the importance of herbivores in coral-reef systems, this study focused on characterising and quantifying the process of herbivory in the NMP with a particular emphasis on the removal of adult macroalgae.
We used a range of approaches to gain an understanding of spatial and species-related patterns in herbivory in five distinct studies. Using underwater video cameras and Sargassum myriocystum assays, 23 different fish species were observed consuming macroalgae, but seven species (Naso unicornis, Kyphosus sp., K. vaigiensis, Siganus doliatus, Scarus ghobban, S. schlegeli and initial-phase Scarus sp.) together accounted for 95% of the observed bites across five regions. Of these species, three were identified as the most important in consuming macroalgae: N. unicornis, Kyphosus sp. and K. vaigiensis. These results were supported by stable isotope analyses that incorporate nutrients from food sources over far longer periods than those examined using the assay approach.
The attached final report provides details on the 5 studies conducted related to herbivory:

Spatial patterns in herbivory on a coral reef are influenced by structural complexity but not by algal traits.
Herbivore diversity on coral reefs: a transcontinental comparison. 
Variation in macroalgal herbivory by fishes across a western-continental coral-reef system. 
Variability in the food sources of herbivorous invertebrates and fishes in a coral-reef system: a stable isotope approach. 
The role of herbivory on the spatial distribution of recruiting and established algal communities in coral versus algal dominated habitats.


Tags: Biosphere | Aquatic Habitat | Benthic Habitat, Biosphere | Ecological Dynamics | Herbivory, Biosphere | Ecological Dynamics | Primary Production, Oceans | Marine Biology | Marine Invertebrates
Organization: Australian Ocean Data Network
Rate of decomposition of crown-of-thorns starfish, Acanthaster planci, on the Great Barrier Reef

The decomposition of 67 crown-of-thorns starfish was monitored in 2 m x 2 m permanent quadrats established at John Brewer Reef in September 1985 and Little Broadhurst Reef in December 1988.Approximately 2 months prior to the commencement of each study, the starfish were kept under starvation conditions in the laboratory to simulate the general state of health that would be expected at the end of outbreaks, when food usually is limited. The starfish were transported back to the reefs and killed by immersion in fresh water for 8 hours.Four quadrats were located amongst patch reefs along the north eastern perimeter of John Brewer Reef. Two of the quadrats were located on sand at 9 m depth while the other two were amongst a mixed coral assemblage (mainly Acropora spp.) at a depth of 3 m. All 4 quadrats were within 10 m of each other and ten starfish were placed randomly in each quadrat and monitored over 9 days. Three quadrats were located on the eastern perimeter of the lagoon at Little Broadhurst Reef. The quadrats were situated next to each other on sand at 9 m depth and 9 starfish were positioned randomly in each quadrat and monitored for 7 days.Quadrats were monitored for about 1 hour each time, normally 3 times during the day and once at night. Maps of each quadrat indicated the position of starfish and their state of decomposition. Changes in the position of starfish were noted as were any instances of predation or other activities which might affect the decomposition process. The main morphological features of some predators were noted for later identification as it was not possible to obtain photographs of these animals.
 This preliminary taphonomic study was undertaken to determine how long the remains of the crown-of-thorns starfish (Acanthaster planci) are recognisable in the field and the factors that are important in the decomposition process.

Organization: Australian Ocean Data Network
WAMSI 2 - Dredging Node - Project 4.5 - Corals of the North West of WA: biogeography and considerations for dredging-related research, Western Australia

The objective of the WAMSI DREDGING SCIENCE NODE Project 4.5 was a review of the range of hard coral taxa and/or growth morphologies that occur in the Pilbara and Kimberley areas in order to inform the choice of organism for the lab experiments in project WAMSI DREDGING SCIENCE NODE Project 4.6. The review accessed information available in the published literature (as identified in searches of standard databases such as ISI Web of Knowledge) as well as searches via Google scholar (for grey material). The review also examine all literature cited during the EIS stages of large scale dredging projects and which has been used to develop water quality thresholds for impact prediction.
Data is in the form of a report, which is a secured (printable, non-editable), searchable, Portable Document Format (PDF) showing the results of the analyses and an excel spreadsheet listing species name location etc.

Organization: Australian Ocean Data Network
Marine Biodiversity Hub: Geoscience Australia

The Marine Biodiversity Hub  project is a collaborative research program funded by the Department of Environment, Water, Heritage and the Arts through the Commonwealth Environment Research Facilities (CERF) program. 
For the Geoscience Australia project team, the project involves working with project partners and stakeholders to:
* collate existing useful marine physical and biological datasets for selected areas of Australia's Exclusive Economic Zone and strategically collect new data;

* analyse this data to develop reliable physical surrogates of benthic habitats and biological communities which can be used to predict patterns of biodiversity in the Australian marine jurisdiction; and

* effectively communicate the results of this research, including access to products and datasets.


Tags: Benthos, Biosphere | Aquatic Habitat | Benthic Habitat, Biosphere | Ecological Dynamics | Community Structure, Intertidal or eulittoral zone, Paleoclimate | Ocean/lake Records | Sediments, Stratification
Organization: Australian Ocean Data Network
Derwent Estuary Ambient Water Quality monitoring program - Site SC

Site SC is sampled monthly by the Derwent Estuary Program as part of the  Derwent Ambient Water Quality monitoring program.
Since 2003, ambient water quality monitoring has been carried out on a monthly basis at up to 28 sites throughout the Derwent estuary by Norske Skog Boyer, Nyrstar Hobart and the State Government. Monitoring is carried out by three different boat-based sampling parties, but is co-ordinated to occur on the same day each month. 
At each site, in-situ field measurements are taken using calibrated sensors for temperature, salinity, pH, dissolved oxygen and turbidity. Water clarity is also measured using a secchi disk. Surface and bottom water samples are collected for analysis of true color, total suspended solids(TSS), total  and dissolved nutrients, organic carbon and zinc. at most sites, depth integrated samples are also collected for chlorophyll a using a plastic tube. Bottom samples in the Middle and Outer estuary are collected using a niskin bottle. Pumps are used in the upper estuary site to fill up the bottles. All water samples are analysed at Analytical Service Tasmania, a National Association of Testing Authorities-accredited laboratory. Monitoring site depth is 2 meters

Tags: Derwent Estuary, Hydrolab Vertical Profiler, Niskin Bottles, Oceans | Ocean Chemistry | Ammonia, Oceans | Ocean Chemistry | Nitrate, Oceans | Ocean Chemistry | Nitrite, Oceans | Ocean Chemistry | Phosphate, Oceans | Ocean Optics | Secchi Depth, Oceans | Salinity/density | Salinity, Oceans | Water Quality | Chlorophyll, Oceans | Water Quality | Conductivity, Oceans | Water Quality | Nitrogen Compounds, Oceans | Water Quality | Oxygen, Oceans | Water Quality | Ph, Oceans | Water Quality | Phosphorous Compounds, Oceans | Water Quality | Suspended Solids, Oceans | Water Quality | Trace Metals, Oceans | Water Quality | Turbidity, Oceans | Water Quality | Water Temperature, Secchi Disks, True Colour, sea_water_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
A new measure of particulate polysaccharides on the Great Barrier Reef

A test using fluorescently labeled concanavalin A (FITC-conA), a lectin (a group of proteins that bind polysaccharides), was used to measure particulate polysaccharides (PPs) at 11 stations on the Great Barrier Reef. In conjunction, 96-well filtration plate technology was used to increase throughput of samples.The experiment tested a number of factors: 5 different concentrations of FITC-conA (5, 10, 20, 30, 40 µg mL-1); differences in average fluorescence (over 4 replicates) of samples using filtered and unfiltered FITC-conA; the effect of increasing incubation period of FITC-conA on fluorescence intensity (for both seasons). Concentrations of transparent exopolymer particles (TEPs) from each site in the wet season were measured using the Alcian blue technique for comparison and verification of levels. PP concentrations were compared to concentrations of chlorophyll a, pheophytin and particulate nitrogen to assess phytoplankton as a possible source of PPs.Samples were collected from each station in the wet (February 2006) and dry seasons (August 2006). Other station parameters recorded were: Secchi depth; total suspended solids (TSS); particulate organic carbon (POC); particulate phosphorous (PP); particulate nitrogen (PN); particulate polysaccharides (PPs); phaeophytin; chlorophyll a.
 To develop a lectin-based method for quantifying a broader scale of particulate polysaccharides to complement the existing Alcian blue method used on transparent exopolymer particles (TEPs).
 Sampling stations: Deloraine, Dent, Edward, Hook, Lindeman, Long, Repulse and Whitsunday Islands; Bait and Hook Reefs; Bluewater.

Organization: Australian Ocean Data Network
Analysis of eReefs water quality scenarios to assess implications of land management for the CoTS initiation zone

R scripts and data files used to process, analyse and visualise eReefs catchment counter-factual scenario model data for the paper, &quot;Kroon, Frederieke J., Joseph R. Crosswell, and Barbara J. Robson. The effect of catchment load reductions on water quality in the crown-of-thorn starfish outbreak initiation zone. Marine Pollution Bulletin 195 (2023): 115255.&quot;
Four R scripts are included:
cots1.R extracts all data from the eReefs model scenario outputs and produces an R data file for each scenario. These intermediate data files are not provided but can be re-created using this script and the original eReefs model data.

cots_reprocess.R puts all six scenarios into one combined dataframe and produces daily_values_all_scenarios3.rda or daily_values_all_scenarios3_large.rda, depending on settings. These intermediate data files are not provided.

ccip_salinity.R extracts salinity from the baseline scenario and adds it to the dataframe for all scenarios, producing daily_values_all_scenarios4.rda or daily_values_all_scenarios4_large.rda, depending on settings. These final data files are provided.

cots_analysis.R produces the figures and tables used in the manuscript.

Data used come from eReefs model counter-factual scenarios produced by CSIRO and available from https://dapds00.nci.org.au/thredds/catalogs/fx3/catalog.html

Organization: Australian Ocean Data Network
Coloured dissolved organic matter dynamics in the Great Barrier Reef

793 discrete measurements were collected on the Great Barrier Reef from coastal and offshore regions from 2004 &ndash; 2017.
Full-depth continuous conductivity-temperature-depth (CTD) profiles were recorded on a Seabird SB19Plus at each site before water sample collection using Niskin bottles. Samples were analysed for chorophyll-a pigment concentration (chl a), inorganic nutrients (NH4+, NO3&minus;/NO2&minus;, and HPO42), particulate organic matter (particulate organic carbon (POC), particulate nitrogen (PN) and particulate phosphorous (PP), coloured dissolved organic matter (CDOM), dissolved organic carbon (DOC), total dissolved nitrogen (TDN) and total dissolved phosphorus (TDP) were collected at discrete sampling depths depending on the water column depth.
Coloured dissolved organic matter was studied to provide information about the characteristics and dynamics of the dissolve organic carbon (DOC) fraction.

Organization: Australian Ocean Data Network
Photographic documentation of some of the impacts of a 1-in-30 year storm on the ocean beach at Collaroy / South Narrabeen, NSW (8th June, 2007)

Friday 8th June 2007 saw a severe weather warning from the Bureau of Meteorology. They warned of winds gusting to 90kph, flash flooding, waves exceeding 5m in the surf zone and significant beach erosion. It was dubbed a 30-year storm, and came as a costly reminder of the devastating power of the natural environment. These photographic images were taken on Wednesday 13th June 2007 and illustrate some of the impacts of the storm on Sydney's beaches. Features include a ~15-18ft vertical scarp in South Narrabeen resulting from enormous storm demand, and exposure of stormwater pipes from Collaroy to Narrabeen.

Tags: Human Dimensions | Infrastructure | Buildings, Oceans | Coastal Processes | Erosion, Oceans | Coastal Processes | Shorelines, Oceans | Coastal Processes | Storm Surge
Organization: Australian Ocean Data Network
BODAS Analysis - Forcing dataset (for MARVL)

The Bluelink Ocean Data Assimilation System (BODAS) is an ensemble optimal interpolation system that uses an ensemble of intraseasonal anomalies from a free running model to estimate the background error covariances (BECs). The ensemble-based BECs are multivariate and inhomogeneous and are shown to reflect the length-scales, the anisotropy and the covariability of mesoscale oceanic processes.
This is purely a description of the forcing dataset used within the MARine Virtual Laboratory (MARVL).

Tags: Oceans | Ocean Circulation | Ocean Currents, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Salinity, Oceans | Sea Surface Height | Sea Surface Height
Organization: Australian Ocean Data Network
Water Flow in Seagrass Ecosystems - Hydrodynamic environment of seagrass meadows

The hydrodynamic environment within the seagrass canopy of Amphibolis griffithii, Posidonia australis, Posidonia sinuosa and mixed Posidonia beds was studied, and compared with a bare sand site (See thumbnail).  Electronic current meters developed by the author (Chapter 2 of thesis) was used to measure water velocity profiles.
In addition, the hydrodynamic regimes of sheltered and exposed Posidonia sinuosa sites were studied, as well as sediment size fraction distribution within a dense Posidonia sinuosa meadow.  These studies were undertaken in Shoalwater Bay located south of Perth, Western Australia.

Tags: 63 617002, 63 617003, 63 618005, Amphibolis griffithii, Oceans | Marine Biology | Marine Plants, Posidonia australis, Posidonia sinuosa
Organization: Australian Ocean Data Network
WAMSI Node 4.3.2 - Ecosystem Modelling - Qualitative modelling of the Swan River Estuary ecosystem

The qualitative model that is being developed for the estuarine ecosystem of the Swan River Estuary  will be used to explore how environmental change due to both anthropogenic and non-anthropogenic factors is likely to affect the ecosystem and to assess the potential for management action to ameliorate adverse impacts.  The study is part of a broader qualitative modelling study, initiated by WAMSI, that encompasses the Swan River Estuary, the Peel-Harvey Estuary and the Leschenault Estuary.

Tags: Biosphere | Aquatic Habitat | Estuarine Habitat
Organization: Australian Ocean Data Network
NSW Water Information

The NSW Government WaterInfo website contains a range of provisional data from a range of State Government agencies concerning NSW rivers and water bodies. This data is generally used for the management of our rivers, storages and the surrounding environment.
Some of the data, since it is measured in the field, is close to real-time. This includes water levels, flow and continuous electrical conductivity (used to assess salinity levels).
Other water quality information is determined by sampling, and is updated nightly when laboratory analyses are complete. Water quality is measured for a variety of projects, each producing purpose-built datasets.
An appropriate level of care needs to be taken when using information from this site. Consideration of the purpose for which the data was collected is required. Time constraints have also meant that rigorous quality control checks have not been undertaken on some of the datasets.

Tags: Hydrosphere | Ground Water | Aquifers, Hydrosphere | Ground Water | Discharge/flow, Hydrosphere | Ground Water | Groundwater Chemistry, Hydrosphere | Ground Water | Springs, Hydrosphere | Surface Water | Lakes, Hydrosphere | Surface Water | Rivers/streams, Hydrosphere | Surface Water | Water Depth, Hydrosphere | Surface Water | Water Yield, NEW SOUTH WALES, Oceans | Bathymetry | Seafloor Topography, Oceans | Water Quality | Ph, Oceans | Water Quality | Toxic Chemicals, Oceans | Water Quality | Turbidity, Oceans | Water Quality | Water Temperature, pH, rainfall_amount, salinity, sea_water_electrical_conductivity, turbidity, water_discharge, water_level, water_temperature
Organization: Australian Ocean Data Network