AndreaBozzo/ceres-open-data-index huggingface dataset:
Marine Futures Project - Rottnest Island - reef habitat

The Marine Futures Project was designed to benchmark the current status of key Western Australian marine ecosystems, based on an improved understanding of the relationship between marine habitats, biodiversity and our use of these values. Approximately 1,500 km2 of seafloor were mapped using hydroacoustics (Reson 8101 Multibeam), and expected benthic habitats "ground-truthed" using towed video transects and baited remote underwater video systems. Both sources of information were then combined in a spatial predictive modelling framework to produce fine-scale habitat maps showing the extent of substrate types, biotic formations, etc.
Surveys took place across 9 study areas, including Rottnest Island, a popular family holiday destination just 20 km off the Perth coast. One of the main drawcards of the island is the diverse marine life inhabiting the surounding waters, which Western Australian locals and tourists can experience by snorkelling, diving, boating and fishing.
The marine environment around Rottnest includes seagrass meadows, kelp-covered reef tops, coral patches, and sponge gardens in deeper water. As a result of the warm, southward flowing Leeuwin Current, the island represents the southern limit of the distributions of many tropical corals and fish. The marine life around Rottnest therefore represents a unique mix of tropical and temperate species and habitats.

Tags: Reef habitat, research vessel
Organization: Australian Ocean Data Network
WAMSI 2 - Dredging Node - Project 5.5.1 - Defining thresholds and indicators of primary producers - Seagrass pressure-response relationships - Experiment 1

Objectives of Project 5.5 are to:
(1) determining the pressure:response relationships that relate the effects of dredging-generated sediments on tropical primary producers, 
(2) examine the pathways, rates and timeframes of recovery from impacts and; 
(3) identify and examine the effects of key environmental variables on the pressure:response relationships and recovery.
Specifically Experiment 1 will be studying "Effect of different intensity, duration &amp; timing of light reductions on seagrasses (Laboratory)"
Measurements included:
Absorbancy Factors
Biomass - Above ground mass (g DW per pot), Below ground mass (g DW per pot), Total plant mass (g DW per pot)
Carbohydrates (%DW) and Starch (%DW)
Growth &amp; Morphology - leaf area (cm2), shoot density (per pot), Shoot production rate (shoots d-1)
Nutrient &amp; isotope data - Leaf ‰ 15 Nitrogen, Leaf ‰ 13 Carbon, Leaf Nitrogen (% DW)    Leaf Carbon (% DW)  Leaf Carbon to Nitrogen ratio (g g-1)
Photosynthesis - Electron transport rate (um photons m-2 s-1), Alpha  (um photons m-2 s-1), Half-saturating irradiance  (um photons m-2 s-1)
Pot Biomass - Pot mass (mass of all plants in a pot, g DW per pot)
Species studied included - Cymodocea serrulata and Halodule uninervis

Tags: Biosphere | Aquatic Habitat | Benthic Habitat, Oceans | Coastal Processes | Sediment Transport, Oceans | Marine Biology | Marine Plants, Oceans | Marine Sediments | Turbidity, Oceans | Water Quality | Light Transmission
Organization: Australian Ocean Data Network
Future Reef MAP - February 2014 (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
Tide gauge deployment, Gannet Cay, southern Great Barrier Reef (SGBR Project 1989-1990)

An Aanderaa WLR was deployed at Gannet Cay (Station GCA).Deployment Details: Date deployed: 24/8/89 (SGBR1) Date recovered: 21/2/90 (SGBR3)Instrument: WLR5 #880Depth: 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
Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata

To evaluate the effects of El Nino driven mass thermal stress on the coral Monitpora digitata during spawning in a severe bleaching year (2016).
32 colonies were collected, from a minimum of 5 - 10 metres apart laterally along the shore. Spawning occurred on 23rd April 2015, where egg-sperm bundles were collected from spawning colonies, total of 9. 
27 of these colonies were re-collected from Hazard Bay in April 2016 and 5 remaining colonies were presumed dead. Colony colouration was assessed using the CoralWatch Color Chart, with photographs alongside each colony at the time of collection.
Spawning occurred on 24th April 2016, and a total of 4 were spawning colonies.
To determine the effects of thermal stress and the presence of bleaching in 2016, the health of coral colonies were measured using methods of effective quantum yield of photosystem II (YII), colony coloration, and Symbiodiniaceae cell density. YII was measured using Pulse Amplitude Modulated fluorometry (PAM) with a fibre optic cable (diving-PAM, Waltz).
Samples from all spawning adults and 10 &ndash; 12 eggs from each colony were genotyped in both 2015 and 2016 through ITS2 amplicon sequencing. Analysis of community composition was achieved through sequence variations, evidence of shuffling of Symbiodiniaceae communities and differences in Symbiont densities and photochemical efficiencies.

Organization: Australian Ocean Data Network
RAN CTD Profile Data - HMAS MELVILLE ProjectID: HI446(B)MEL_M From: 2008-10-29 To: 2008-12-05

This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 32 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI446(B)MEL_M from HMAS MELVILLE.
The CTD was manufactured by Applied Microsystems Limited and is the "Micro CTD" model. This CTD type is referred to operationally as the MVP200_CTD. This CTD is fitted with a 4 electrode platinized conductivity cell, thermistor temperature sensor and a semiconductor strain gauge pressure sensor.
The CTD sensors are calibrated at the manufacturer Applied Microsystems Limited on a 12-18 month schedule. The CTD temperature sensor is calibrated against 'Hart' temperature standards. The pressure sensor is calibrated using 'Budenburg Deadweight' standards. The conductivity sensor is calibrated using 'Hart' temperature standards and seawater samples of known conductivity.
The CTD sensors are mounted to a fish-shape probe. The probe is controlled by an electric winch (MVP200 type). For downcasts the fish is allowed to free-fall (winch is in 'free-wheel' mode) under its own weight at about 2-3 ms-1 and then is winched back. Data is recorded in downcast and usually in upcast direction at a sampling rate of 25 Hz. The downcast data is of higher quality because sensors encounter undisturbed seawater that flows through the nose of the fish. On the upcast the fish is flipped around (tail first) and the sensors in the nose encounter disturbed flow from the fish tail.
This type of CTD is prone to a phenomenon called 'salinity spiking' caused by a mismatch between the response times of the temperature and conductivity sensor. Data undergoes a salinity de-spiking routine to correct for this. See the history metadata for further details on the salinity de-spiking process.
Raw CTD pressure data is not always monotonic due to transient up/down motion of winch/ship. Raw pressure data is subsetted to give a monotonic (increasing) sequence and then linearly interpolated to 1 decibar pressure intervals. Data is then flagged with quality control flags after visual inspection and comparison to average climatology and historical CTD casts.

Tags: Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Salinity, sea_water_practical_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
SAIMOS - Biological and Flow Cytometry data collected from CTD stations in South Australia, in March 2010

Flow cytometry data was collected in March 2010, in waters off South Australia. 
The general purpose of the study is to be able to establish background knowledge on the ecosystem on the continental shelf of South Australia and the impact of upwelling/saline outflow events on microbial communities to ultimately develop a biogeochemical model of the region. Sampling was carried out during cruises conducted on board the RV Ngerin as part of the Southern Australian Integrated Marine System (SAIMOS). During each cruise, the physical, chemical and biological properties of the chlorophyll fluorescence maximum (FM) layer were investigated. Flow cytometry data has been collected for picophytoplankton, bacteria and viruses.
Six main stations have been sampled over the course of the study, five are located on the 100 m isobath, i.e. RS (35.508S, 136.278E), B2 (35.418S, 136.148E), B3 (35.258S, 136.048E), B4 (35.168S, 135.418E) and B5 (35.008S, 135.198E), and one from an offshore station (B1; 36.188S, 136.178E) located southwest of Kangaroo Island. Note that combining the distances between stations (14–25 nautical miles), the average component of the current velocity at middepth along the shelf (0.01 m s21) and the average speed of the vessel (i.e. 9 knots) indicate that different water masses were sampled at each station. Additional samples have on occasion been collected from the National Reference Station (NRS) at Kangaroo Island (35.832S, 136.447E) and the SA Spencer Gulf Mouth Mooring (SAM8SG, 35.25S, 136.690E), where the saline outflow occurs.

Tags: Biosphere | Microbiota | Bacteria, Biosphere | Vegetation | Phytoplankton, IMOS Node | SA-IMOS | Southern Australian Integrated Marine Observing System, Niskin Bottles, Oceans | Bathymetry | Water Depth, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Chemistry | Inorganic Matter, Oceans | Ocean Chemistry | Nitrogen, Oceans | Ocean Chemistry | Organic Matter, Oceans | Ocean Chemistry | Phosphate, Oceans | Ocean Chemistry | Silicate, Oceans | Ocean Chemistry | Suspended Solids, Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Ocean Winds | Surface Winds, Picophytoplankton, Virus, amount_of_bacteria_in_sea_water, amount_of_picophytoplankton_in_sea_water, amount_of_virus_in_sea_water, concentration_of_chlorophyll_in_sea_water, depth, depth_of_chlorophyll_maximum, latitude, longitude, mass_concentration_of_particulate_inorganic_matter_in_sea_water, mass_concentration_of_particulate_organic_matter_in_sea_water, mass_concentration_of_suspended_matter_in_sea_water, mole_concentration_of_nitrogen_in_ammonium_in_sea_water, mole_concentration_of_nitrogen_in_nitrate_and_nitrite_in_sea_water, mole_concentration_of_phosphorus_in_phosphate_in_sea_water, mole_concentration_of_silicate_in_sea_water, sea_surface_temperature, wind_from_direction, wind_speed
Organization: Australian Ocean Data Network
Owner Advantage in the fiddler crab, Uca mjoebergi. Fight data between burrow owners and natural floaters

Resource owners generally win contests against intruders, a phenomenon referred to as the 'Owner Advantage' (OA). Uca mjoebergi is a typical fiddler crab that is highly sociable, territorial and lives in mixed sex colonies on intertidal mudflats. Burrows are used in territory defence, for mating, and as refuge from predators and environmental stresses. Fights are common between owners and floating males who battle for ownership of the territory and burrow. 
Experiments were conducted from 28th Sept - 30 Dec 2006 at the lower reaches of Ludmilla Creek within East Point Reserve, 5km North of Darwin, NT. This experiment found that when attacked by naturally occurring floaters, owners were most likely to win fights. Owners won 91.9% of fights against naturally occurring floaters. There is therefore a strong ownership advantage in this species.

Tags: 28960043, Biosphere | Ecological Dynamics | Community Structure, Biosphere | Ecological Dynamics | Competition, Biosphere | Ecological Dynamics | Dominance, Biosphere | Zoology | Crustaceans, Fiddler crabs, Owner Advantage, Uca mjoebergi
Organization: Australian Ocean Data Network
Zooxanthellate scleractinian corals of northwestern Madagascar (Marine RAP survey)

Zooxanthellate scleractinian corals were surveyed at 29 sites in north west Madagascar in 2002, using rapid assessment methods. Surveys were conducted using SCUBA to a maximum depth of 44m and covered a wide range of habitats. Seven sites were surveyed at two depths: one deep (&gt;12m) and one shallow (0 to 8-12m).Most species were identified visually, underwater. Where taxonomic or identification problems arose, samples were collected for further examination. A large number of these specimens were sent to the Australian Institute of Marine Science for comparison with reference collections and positive identification.
 The aims of this survey were:1. to build a cumulative total of zooxanthellate scleractinian coral species for the entire study area2. to provide information to allow comparisons with previous records for Madagascar and the SW Indian Ocean
 The Marine Rapid Assessment Program (RAP) is an initiative of Conservation International (CI). This survey was a component of the project "A rapid marine biodiversity assessment of the coral reefs of northwest Madagascar".

Organization: Australian Ocean Data Network
Biological and chemical oceanographic measurements from Western Australia and Northern Territory shelf waters

An extensive series of hydrographic and biological oceanographic measurements were made on the transit legs of the RV Lady Basten in July-August 1993 and October-November 1993 in North Western Australia. The westward route proceeded across the Timor Sea from Darwin to Scott Reef and after a series of biological oceanographic measurements and oceanographic instrument deployments at that site, to Dampier. On the return voyage, the scientific party aboard the Lady Basten made further biological measurements at sites near Scott Reef, then carried out an extensive program of water sampling along the Kimberley coast before proceeding east across the Timor Sea to Darwin.
In all, 68 hydrographic stations were sampled in the Timor Sea and on the North West Shelf. Water column primary production measurements were made at 16 of these stations and bacterial production measurements at 16 stations.
Measurements made at sampling stations along the transit route included:

Water column temperature, salinity and density structure
Dissolved and particulate nutrient (N, P, Si) concentrations
Phytoplankton biomass and community size structure
Zooplankton standing crop and composition
Water column primary production
Water column bacteria numbers and biomass (westward leg only)
Water column bacterial production (westward leg only)
Trichodesmium abundance and distribution
N fixation by Trichodesmium (eastward leg only)


Organization: Australian Ocean Data Network
ERIN Dual-processed Landsat TM tiles in Western Australia - Collie tile

A Landsat TM image was cut using a NATMAP Geoscience Australia 1:250 000 scale map named Collie (Map number SI50-6) and was saved in GeoTIFF format.
The image was geometrically rectified to GDA94 (Datum) and MGA50 (Projection) and a dual enhancement technique was conducted to Landsat TM satellite data where land was enhanced using bands 741 (RGB) and water was enhanced using bands 321 (RGB).  This is one of a series of tiles processed by ERIN from Coastal Atlas project in the 1990's.

Organization: Australian Ocean Data Network
SAIMOS - Biological and Flow Cytometry data collected from CTD stations in South Australia, in May 2014

Flow cytometry data was collected in May 2014, in waters off South Australia. 
The general purpose of the study is to be able to establish background knowledge on the ecosystem on the continental shelf of South Australia and the impact of upwelling/saline outflow events on microbial communities to ultimately develop a biogeochemical model of the region. Sampling was carried out during cruises conducted on board the RV Ngerin as part of the Southern Australian Integrated Marine System (SAIMOS). During each cruise, the physical, chemical and biological properties of the chlorophyll fluorescence maximum (DCM) layer were investigated. Flow cytometry data has been collected for picophytoplankton, bacteria and viruses.
Six main stations have been sampled over the course of the study, five are located on the 100 m isobath, i.e. RS (35.508S, 136.278E), B2 (35.418S, 136.148E), B3 (35.258S, 136.048E), SAM2CP/B4 (35.168S, 135.418E) and SAM5CB/B5 (35.008S, 135.198E), and one from an offshore station (B1; 36.188S, 136.178E) located southwest of Kangaroo Island. Note that combining the distances between stations (14–25 nautical miles), the average component of the current velocity at middepth along the shelf (0.01 m s21) and the average speed of the vessel (i.e. 9 knots) indicate that different water masses were sampled at each station. Additional samples have on occasion been collected from the National Reference Station (NRS) at Kangaroo Island (35.832S, 136.447E) and the SA Spencer Gulf Mouth Mooring (SAM8SG, 35.25S, 136.690E), where the saline outflow occurs.

Tags: Biosphere | Microbiota | Bacteria, Biosphere | Vegetation | Phytoplankton, IMOS Node | SA-IMOS | Southern Australian Integrated Marine Observing System, Niskin Bottles, Oceans | Bathymetry | Water Depth, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Chemistry | Inorganic Matter, Oceans | Ocean Chemistry | Nitrogen, Oceans | Ocean Chemistry | Organic Matter, Oceans | Ocean Chemistry | Phosphate, Oceans | Ocean Chemistry | Silicate, Oceans | Ocean Chemistry | Suspended Solids, Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Ocean Winds | Surface Winds, Picophytoplankton, Virus, amount_of_bacteria_in_sea_water, amount_of_picophytoplankton_in_sea_water, amount_of_virus_in_sea_water, concentration_of_chlorophyll_in_sea_water, depth, depth_of_chlorophyll_maximum, latitude, longitude, mass_concentration_of_particulate_inorganic_matter_in_sea_water, mass_concentration_of_particulate_organic_matter_in_sea_water, mass_concentration_of_suspended_matter_in_sea_water, mole_concentration_of_nitrogen_in_ammonium_in_sea_water, mole_concentration_of_nitrogen_in_nitrate_and_nitrite_in_sea_water, mole_concentration_of_phosphorus_in_phosphate_in_sea_water, mole_concentration_of_silicate_in_sea_water, sea_surface_temperature, wind_from_direction, wind_speed
Organization: Australian Ocean Data Network
Genetics of two species of soft coral, Sinularia flexibilis and Clavularia koellikeri, from the Great Barrier Reef

The genetic structure of 12 reef populations of the soft coral Sinularia flexibilis was studied along the Great Barrier Reef (maximum separation 1300 km). Up to 64 individuals per reef were collected at at 2 or 3 sites per reef, at a minimum of 5 m apart. Collection locations were: Dungeness, Cumberland, Pickersgill, Escape, Agincourt, Undine, Orpheus, Trunk, Rib, Cannon Bay, Deloraine, Hook Island. In two of these sectors, pairs of inshore and mid/offshore reefs were sampled.Electrophoretic analysis of 9 polymorphic allozymes (GPI, HK, FBP, TPI, ME, MDH, VL, LGG, FLE) was made.Departures of genotypic frequencies were evaluated for each locus using the Monte Carlo method using TFPGA software.Genetic diversity and sexual versus asexual contributions to populations were further evaluated of multi-locus genotypes using:1. Observed and expected genotype diversity ratios (Go:Ge).2. Ratio of the [estimated] number of all individuals generated by sexual reproduction (N*) to the number of individuals (N).3. Number of genotypes observed (Ngo) over N.Spatial autocorrelation of genotypes within reefs was also investigated using Moran's I and Geary's c calculations.To investigate the contribution of sexual and asexual reproduction in the soft coral Clavularia koellikeri (Octocorallia: Alcyonacea, Clavulariidae), populations were collected at ten sites among six reefs from two well-separated regions of the Torres Straits (Dungeness, Zuna, Wednesday Is), and the Great Barrier Reef (GBR; Pandora Reef, Orpheus Island, Britomart Reef), Australia. Eight allozyme loci were analysed. Genetic diversity was lower in the southern (18 degrees S) compared with the northern (10 degrees S) populations, suggesting that reefs closer to the southernmost limit of the distribution of C. koellikeri within the GBR (19 degrees S) may represent a more marginal habitat for this species. High levels of genetic differentiation were significant at all spatial scales (sites within reefs, reefs, and regions) from &lt;4 km up to 1,000 km, indicating that C. koellikeri has limited dispersal, consistent with having brooded larvae.
 To investigate the relative importance of sexual and asexual reproduction, genetic differentiation and gene flow among these populations.
 Initial screening of 30 enzymes showed the 9 enzymes could be used for routine screening based on their resolution, polymorphism, and reliability of scoring for S. flexibilis, and eight for C. koellikeri.

Organization: Australian Ocean Data Network
WAMSI Node 3.1.1b and 3.2.2 - Ecosystem Effects of Fishing: finescale coral reef fish surveys Ningaloo Reef - Osprey Reference

From 2006 to 2007 at northern Ningaloo Reef, stereo Baited Remote Underwater Video (stereo-BRUVs) and stereo Diver Operated Video (stereo-DOVs) were used to measure fish assemblages across shallow coral reef lagoon habitats. Four areas were identified including Osprey and Mandu Sanctuary, and Osprey and Mandu Reference Areas which were studied with stereo-BRUV and stereo DOV transects, during two successive summer and winter periods. Each time, six stereo BRUVs and 5 stereo-DOV transects were collected from within 6 coral reef lagoon habitats at 2 well established sanctuary zones and adjacent areas.  The video footage was used to create the raw abundance and length data of different fish species.

Tags: Biosphere | Aquatic Habitat | Reef Habitat, Oceans | Marine Biology | Fish
Organization: Australian Ocean Data Network