AndreaBozzo/ceres-open-data-index huggingface dataset:
SAIMOS - Biological and Flow Cytometry data collected from CTD stations in South Australia, in December 2011

Flow cytometry data was collected in December 2011, 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), 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
Predator-Prey Interactions, Foraging Ecology and Stable Isotope Analysis of Green Sea Turtles (Chelonia mydas) in Shark Bay, Western Australia

I will examine the impacts of green turtle foraging on sea grass beds and the potential behaviorally mediated indirect interaction (BMII) of tiger sharks on sea grass beds via green turtle foraging behavior and habitat use.

Tags: Biosphere | Ecological Dynamics | Feeding Habitat, Biosphere | Ecological Dynamics | Predation, Chelonia mydas, Green Turtles, Marine Features (Australia) | Shark Bay, WA, Predator-Prey Interactions, Seagrass, Stable Isotopes, Tiger Sharks
Organization: Australian Ocean Data Network
Current meter deployments, North Reef, southern Great Barrier Reef (SGBR Project 1989-1990)

An acoustic current meter, an Aanderaa RCM7 rotary current meter and an Aanderaa RCM5S rotary current meter were deployed on a single mooring at North Reef (Station CM3). Two consecutive deployments of these current meters were made in 152 meters of water. Deployment 1: Date deployed: 29/8/89 (SGBR1) Date recovered: 24/10/89 (SGBR2)Instruments:SACM; Depth: 12m; Deployment Code: NT11RCM7 #9139; Depth: 22m; Deployment Code: NT12RCM5S #7350; Depth: 77m; Deployment Code: NT13Deployment 2: Date deployed: 24/10/89 (SGBR2) Date recovered: 24/02/90(SGBR3)Instruments:SACM; Depth: 82m; Deployment Code: NT21RCM7 #9139; Depth: 92m; Deployment Code: NT22RCM5S #7350; Depth: 147m; Deployment Code: NT23Sampling Intervals:SACM: 60 mins integrating for 20 min centered on the hourRCM7: 60 minsRCM5S: 60 mins with 16 revs per count
 These deployments were components of the SGBR Project 1989-1990.

Organization: Australian Ocean Data Network
NOAA - Australasian Surface Drifting Buoys

This dataset contains the tracks of surface drifting buoys in the Australasian region, deployed as part of the Global Drifter Program (GDP). The GDP collects operational, near-real time surface velocity, sea surface temperature (SST), sea surface salinity, and sea level pressure observations (not presented here) for numerical weather forecasting, research, and in-situ calibration/verification of satellite observations. The GDP is managed in close cooperation between the NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML) in Miami, Florida, and the branch of the NOAA Cooperative Institute for Marine Ecosystems and Climate (CIMEC) located at the Scripps Institution of Oceanography in La Jolla, California.
Access to the data (not updated since 2014), represented by this metadata record, has been removed from the AODN Portal (09/08/2021).

Tags: Continents | Africa, Continents | Asia, Continents | South America, Countries | Australia, Countries | China, Countries | Fiji, Countries | India, Countries | Indonesia, Countries | Madagascar, Countries | Malaysia, Countries | New Caledonia, Countries | New Zealand, Countries | Papua New Guinea, Countries | Philippines, Countries | Sri Lanka, Countries | Thailand, Countries | Timor-Leste, Countries | Vanuatu, Countries | Vietnam, Global / Oceans | Atlantic Ocean, 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 | Bay of Bengal, Oceans | Ocean Pressure | Water Pressure, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/Density | Salinity, Regional Seas | Arabian Sea, Regional Seas | Arafura Sea, Regional Seas | Banda Sea, Regional Seas | Celebes Sea, Regional Seas | Coral Sea, Regional Seas | Java Sea, Regional Seas | Mozambique Channel, Regional Seas | Philippine Sea, Regional Seas | Solomon Sea, Regional Seas | South China Sea, Regional Seas | Tasman Sea, Regional Seas | Timor Sea
Organization: Australian Ocean Data Network
The physical environment of Scott Reef, Western Australia (2003): South Scott Reef, East Hook Transect (H)

Six instruments were deployed on the South Scott Reef, East Hook Transect (H). Instruments were deployed along a transect down the reef slope.Code: EH6; Depth: 1.9m; Instrument: Odyssey; Serial #: 6537;Code: EH5; Depth: 1.2m; Instrument: Odyssey; Serial #: 6540; Code: EH4; Depth: 2.2m; Instrument: Odyssey; Serial #: 6549;Code: EH3; Depth: 6.3m; Instrument: Tidbit; Serial #: SL1-1;Code: EH2; Depth: 10m; Instrument: Odyssey; Serial #: 6557;Code: EH1; Depth: 19.7m; Instrument: AQD; Serial #: 1015; File Name: EH1uvm
 This deployment was a component of the "Physical Environment" sub-project of the project "Biological and Physical Environment at Scott Reef 2003"

Organization: Australian Ocean Data Network
Land Surface Temperature Mid Miocene.

The data are of a simulated land only surface temperature difference between the middle Miocene at 15 million years ago and present day with US NCAR climate models. The data includes all available monthly sea surface temperature measurements from 1900 to 2000. The results recreate the temperature of 15 million years, ago which correlates to similar predictions for future climate warming.
The areas of significant temperature increase (over 6 deg C) shown are in northern America and Europe. In  Western and Southern Australia, Miocene temperature was 6 C higher than present, and likely due to a stronger Leeuwin Current carrying a greater amount of equatorial water from the tropics since the Indonesian sea straits were wider and the Indonesian throughflow could be stronger. The middle Miocene Climate Optimum at 15 ma is the most recent warming event in geological history. The results suggest that our planet is heading back to the middle Miocene climate but with a different mechanism.

Tags: Oceans | Ocean Temperature | Sea Surface Temperature, ground_temperature
Organization: Australian Ocean Data Network
Nephelometer data sets for Dredge_East 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: Nephelometer, Oceans | Marine Sediments | Sedimentation, Oceans | Marine Sediments | Turbidity, suspended_sediment_concentration
Organization: Australian Ocean Data Network
The relative abundance (%) of planktonic foraminifera over time in core MD032607, located off the coast South Australia

The advent of deep-sea drilling in the 1950's prompted the use of planktonic foraminifera (unicellular protozans) as palaeoceanographic indicators. They provide a natural archive of past environmental changes due to their global distribution, their prolific productivity and sensitivity to environmental variations.The highest species abundance of foraminifera in core MD032607 was recorded by Globigerina bulloides (~45%) during the penultimate glacial period (MIS 6) and, generally, was the most abundant with an average abundance of 19.5%. The dominance of the sub-polar, transitional species, Ga. bulloides in this core suggests the influence of cold, nutrient-rich water during certain isotopic stages. Conversely, the dominant warm and oligotrophic species Globigerinoides ruber recorded its lowest abundance in Marine Isotope Stage (MIS) 6, and is totally removed from the record (0%) at 146K, 142K, and 139K yrs BP.

Tags: Biosphere | Ecological Dynamics | Population Dynamics, Biosphere | Microbiota | Foraminifers, age_of_core, taxonomic_group_count
Organization: Australian Ocean Data Network
Large Initial-Condition Earth System Model Ensembles (LEs) Model Intercomparison Project (LE-MIP)

The US CLIVAR Working Group on Large "Initial-Condition" Earth System Model Ensembles (LEs) was formed in March 2018. The intent of the working group is to spearhead a dedicated effort across the national and international climate communities to advance progress on identifying anthropogenic influences on weather and climate amidst the "noise" of internal variability. The timeliness and cross-cutting nature of the problem, together with promising new observational and modelling approaches, means this working group has an unprecedented opportunity to make substantive progress on this tractable issue. Reference: https://usclivar.org/working-groups/large-ensemble-working-group?
The Australian contribution to the LE-MIP includes output derived from the CSIRO-MK3-6-0 model and covers historical and rcp85 scenarios, described in Rotstayn, L. D., Jeffrey, S. J., Collier, M. A., Dravitzki, S. M., Hirst, A. C., Syktus, J. I., and Wong, K. K. (2012). Aerosol- and greenhouse gas-induced changes in summer rainfall and circulation in the Australasian region: a study using single-forcing climate simulations, Atmos. Chem. Phys., 12, 6377-6404, doi:10.5194/acp-12-6377-2012.
Note that the first 10 ensembles or experiments of LE-MIP were published as one model within the CMIP5 multi-model submission, however, the metadata has been modified somewhat to reflect the LE-MIP set. The LE-MIP parameter list/set is a smaller subset of that submitted to CMIP5, however, daily sets are available for all years compared to typically only a few specific year ranges in CMIP5.

Tags: 0401 - Atmospheric Sciences, 040104 - Climate Change Processes, 040503 - Physical Oceanography, Climate Model, Ensemble, Initial Condition, LE-MIP
Organization: Australian Ocean Data Network
SAIMOS - Biological and Flow Cytometry data collected from CTD stations in South Australia, in November 2011

Flow cytometry data was collected in November 2011, 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), 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
Photochemical decomposition rates of pteridines and flavins in seawater from Rib Reef, Great Barrier Reef

Photochemical decomposition rates of pteridines and flavins in seawater from Rib Reef were determined by reverse-phase liquid chromotography with fluorometric detection. The water was exposed to ambient surface solar radiation and samples removed at various time intervals [?2 hr before noon, noon, 2 hr after noon?] and direct injection (10-100µl) HPLC analyses conducted. For each component, the fluorescent transformation products were identified along with quantity, and the first-order decomposition rates (sea water, distilled water, distilled water with Cu2+ ion) measured.
 To examine the ecological significance of the occurrence, influence and fate of pteridines and flavins in coral reef waters.
 Pteridines: 6-biopterin, 6-hydroxymethylpterin, folic acid, isoxanthopterin, pterin, pterin-6-carboxylic acid, xanthopterin.Flavins: lumichrome, lumiflavin, riboflavin, riboflavin-5-phosphate.

Organization: Australian Ocean Data Network
Effect of Habitat Change: Foraging habitat use and prey resources of bottlenose dolphin in Cockburn Sound

Field studies of dolphin foraging behaviour were carried out between 2000 and 2002 in Cockburn Sound with two objectives:
1) to quantify the foraging habitat use of dolphins within Cockburn Sound and;
2) to identify the spatial and temporal patterns of large (10+ individuals) aggregrations of foraging dolphins.

Tags: 41 116019, 41 116020, Biosphere | Ecological Dynamics | Feeding Habitat, Oceans | Marine Biology | Marine Mammals, Tursiops aduncus, Tursiops truncatus
Organization: Australian Ocean Data Network
Coffin Bay CTD Data 24 September 1998

Six samples were collected at Coffin Bay using a conductivity-temperature-depth (CTD) device on 24th September 1998, for analysis of water temperature, conductivity, and salinity data.

Tags: Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Salinity, depth, sea_water_electrical_conductivity, sea_water_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
Sensitivity of live microalgal aquaculture feed to singlet oxygen-based photodynamic therapy

The manuscript builds on work performed as part of the PhD project of AIMS@JCU PhD student Danilo Malara. Thesis title: Photodynamic antimicrobial chemotherapy for pathogenic Vibrio control in prawn hatcheries. Chapter 4: Sensitivity of live microalgal aquaculture feed to photo antimicrobial chemotherapy.  JCU supervisors were Kirsten Heimann and Michael Oelgemoeller.
Summary and Importance:
Photodynamic antimicrobial chemotherapy is an emerging sterilization technique based on chemical compounds activated by light.
We tested the suitability of this technique for cleaning up bacteria growing in microalgae cultures used as feed in aquaculture.
We found that the cell wall of the microalgae determines if the technique is toxic to the microalgae itself.
The techniques is suitable for sterilising only one of the tested microalgae-species, Nannochloropsis oculata.
Instead, the technique has potential for killing unwanted microalgae in aquaria and aquaculture facilities, but this would require further studies.
Description of experiments:
An experiment was performed at JCU using a cationic porphyrin (TMPyP) as the photosensitizer and the following microalgae cultures: Tisochrysis lutea, Nannochloropsis oculata, Tetraselmis chui, Picochlorum atomus, Chaetoceros muelleri. A range of porphyrin concentrations (0 - 50 micromolar) and treatment times (1 - 6 hours) were tested for each microalgae species.
Only Nannochloropsis oculata was resistant to the porphyrin treatment. This species was used in a disinfection experiment, where bacterial contamination was simulated by adding a naturally luminescent bacterium, Vibrio campbellii ISO7, at three different concentrations (1E3 CFUs/ml, 1E5 CFUs/ml, 1E7 CFUs/ml). In each case, an optimised disinfection protocol (based on experiments described above) was used with 20 micromolar porphyrin and 6 hour treatment.
The disinfection experiment itself, including the inoculation of agar plates and most probable number (MPN) enrichment cultures, was done at JCU. Sealed agar plates and boiled cell pellets were brought to AIMS for visualisation of luminescent colonies on the gel doc system and for multiplex PCR, respectively.
The data set includes:
Flow cytometry data to determine microalgae viability.
Dry weight and cell count determination of microalgae culture for biomass standardisation.
Plate reader data (luminescence) to determine the concentration of the bacterial pure culture.
Photos of agar plates showing luminescent bacterial colonies (added model bacterium)
Gel photos showing results of multiplex PCRs of MPN-enrichment cultures (to quantify added model bacterium).

Organization: Australian Ocean Data Network
Temperate Australian quantitative spatial and temporal abundance data for rocky reef biota (biodiversity): Batemans Bay (NSW)

The data is quantitative abundance of fish and megafaunal invertebrates and algal % cover derived from transect based counts at a wide range of locations across Temperate Australia. The methods are described in detail in Edgar and Barrett (1997). Primarily the data are derived from transects at 5 m depth and/or 10 m depth at each site surveyed. Methods were initially developed for research on temporal changes following protection in Tasmanian MPAs (Maria Is, Tinderbox, Ninepin Point, Governor Island). The data represented by this record was collected in MPA studies and surveys interstate, and was collected from Batemans Bay (NSW). In many cases the dataset involved temporal replication (year scale).

Tags: Abundance - fish, Abundance - invertebrates, Carapace length - rock lobster, Fish size class, Percentage cover algal species, Shell length - abalone
Organization: Australian Ocean Data Network
Tertiary Sediment Cell Boundary

Sediment cells are spatially discrete areas of the coast within which marine and terrestrial landforms are likely to be connected through processes of sediment exchange, often described using sediment budgets. They include areas of sediment supply (sources), sediment loss (sinks), and the sediment transport processes linking them (pathways). Sediment transport pathways include both alongshore and cross-shore processes, and therefore cells are best represented in two-dimensions. They are natural management units with a physical basis and commonly cross jurisdictional boundaries. Further information can be found at the following website: http://www.transport.wa.gov.au/imarine/coastal-erosion-and-stability.asp

Tags: DoT, Downloadable Data, WA, australia, beach, beachface, blowout, cell, change, coast, coastal, coastal access, coastal engineering, department of transport, development, drift, dune, dynamic, ecosystem, foreshore, littoral, management, marine, movements, ocean, planning, protection, sand, sea, sediment, shift, shoreline, transport, vegetation, water, waterline, western australia, year
Organization: Australian Ocean Data Network
Predictive models for the selection of thermally tolerant corals based on offspring survival

Wild corals were collected on the Northern and Central regions of the Great Barrier Reef at depths of ~4m. The colonies were transferred to the National Sea Simulator at AIMS. Spawning occurred on 26th to the 29th of November 2018, and experiments were carried out from Nov 2018 until March 2019.
Thermal heat test experiments were conducted following coral spawning and purebred / hybrid offspring were produced. Larvae were reared and subjected to a heat tests. Larval survival was counted from 0 to 56 hours at 27&deg;C and 35.5&deg;C.
Larvae were then induced to settle, exposed to symbionts and then exposed to heat stress. Both larvae and juveniles were sampled for survival, counted at 0 and after 58 days at 27 and 32&deg;C treatments.
Individual larvae were counted within replicate net-wells, in replicate, plates within each temperature treatment. Each larval survival measurement represents a discrete sample measurement.
Juvenile survival, bleaching and growth were assessed, survival statistical analyses were run in R (v. 3.6.0) and amplicon Miseq and RNAseq sequencing of Symbiodiniaceae taxa in coral juveniles.
See Quigley &amp; van Oppen (2022) for full details.

Organization: Australian Ocean Data Network