AndreaBozzo/ceres-open-data-index huggingface dataset:
Environmental DNA (eDNA) survey of Bathurst Harbour (Tasmania) for the endangered Maugean skate (Zearaja maugeana) (NESP MaC 1.33)

The Maugean Skate Zearaja maugeana is a micro-endemic species known from only two isolated estuaries, Bathurst and Macquarie Harbours in southwestern/western Tasmania. This constitutes one of the most limited distributions of any known extant elasmobranch. As a result, the species is listed as ‘Endangered’ under the Threatened Species Protection Act (Tasmania) and the Environmental Protection and Biodiversity Conservation Act (Commonwealth). 
Even though it was first discovered in Bathurst Harbour, most of what is known about the species comes from the Macquarie Harbour population. Only four individuals have ever been reported in Bathurst Harbour, with the last known sighting occurring in 1992. 
This study used environmental DNA (eDNA) to determine the presence/absence of the Maugean skate in Bathurst Harbour on the southwest coast of Tasmania.
Water samples were collected from the seafloor in Bathurst Harbour in November 2021 and February 2022, and in Macquarie Harbour (control samples) in December 2021. Samples were filtered using a self-preserving eDNA sampling system. Following each survey DNA from the samples was extracted and analysed through qPCR amplification. Mitochondrial primer pairs from two gene regions were used to detect the presence of Maugean skate DNA in the samples. Where possible, positive detections were sequenced, and their identity verified.

Tags: Bathurst Harbour, Macquarie Harbour, Maugean skate, National Environmental Science Program (NESP) Marine and Coastal Hub, Zearaja maugeana, eDNA
Organization: Australian Ocean Data Network
Microbial and chemical patterns during a disease outbreak in the sponge, Aplysina aerophoba, from Slovenia

Samples of Aplysina aerophoba were collected by scuba at 3-7 m depth at Pacug, Slovenia for microbiological and chemical comparison between sponge lesions and unaffected tissue on 10 diseased sponges and 10 healthy controls. To estimate disease incidence, a survey was performed along a randomly selected 15m line transect: all healthy and diseased specimens found within 0.5 m to either side were recorded: 53 Aplysina aerophoba colonies were recorded of which, 22 presented visible disease symptoms (black patches, white necrotic tissue or exposed skeletal fibres).DGGE was used to explore the similarity in microbial communities between healthy and diseased samples. A total of 65 unique bands were used to compare community similarity between samples, of these, 24 were sequenced to obtain phylogenetic detail. 16S rRNA gene sequencing disclosed bacterial phyla with representatives of the Alpha-, Gamma-, Delta- and Epsilon-proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes and Cyanobacteria. The Bacteroidetes (13, 19 and 21) and Epsilonproteobacteria (20 and 24) were only detected in diseased sponges.A more comprehensive phylogenetic comparison between the diseased and healthy samples using clone sequence data showed considerable differences proportions of the microbial community composition. Rarefaction analysis was performed to determine the number of unique bacterial clones as a proportion of the estimated total diversity.To determine if any eukaryotic organisms were specifically associated with the lesions on Aplysina aerophoba, DGGE was conducted with universal eukaryotic primers. A large number of bands were detected, but a single band was present in all diseased samples (with the exception of D2) and absent from the unaffected tissue of diseased sponges and healthy controls. 18S rRNA gene sequencing of this band revealed 96% sequence homology to the Harpactic copepod, Tisbe furcata.A maximum-likelihood phylogenetic tree was constructed from analysis of all 16S rRNA gene sequences retrieved from DGGE analysis. HPLC-UV-MS was used to acquire chemical profiles of healthy, diseased and unaffected portions of diseased Aplysina aerophoba tissue.
 The study aimed to understand the microbiology associated with 'Aplysina Black Patch Syndrome' and to determine if shifts in sponge metabolite production occur with disease.

Organization: Australian Ocean Data Network
RAN CTD Profile Data - HMAS MELVILLE ProjectID: SRATA-0135MEL_M From: 2008-01-17 To: 2008-01-20

This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 86 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise SRATA-0135MEL_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
Derwent Estuary Recreational Water Quality monitoring program - Nutgrove Beach West

Nutgrove Beach West monitoring site is collected as part of the Derwent Beach Watch program. Derwent Beach Watch is a collaborative program between councils and state government that tests water quality at 18 swimming sites around the estuary during summer months. 
Water samples are collected each Tuesday from the start of December to the end of March and analysed for the faecal indicator bacteria Enterococci (Enteralert method) at the Public health Lab. Because the samples must be cultured, it takes several days to publish the results.

Tags: Derwent Estuary, Hydrolab Vertical Profiler, Oceans | Salinity/density | Salinity, Oceans | Water Quality | Contaminants, Oceans | Water Quality | Ph, Oceans | Water Quality | Turbidity, Oceans | Water Quality | Water Temperature, Water Quality Monitoring, sea_water_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
Marine Biological Survey of the Central Kimberley Coast, Western Australia

To document the marine flora and fauna of the Kimberley region, and to make the information available to the public and scientific community.
Survey focused on islands and reefs between Montgomery Island and Cassini Island.  NOTE: survey boundary was not defined in report

Tags: Biosphere | Vegetation | Vegetation Species, Fauna, Field Surveys | Biological Surveys, Flora, Marine Features (Australia) | Kimberley Coast, WA, Oceans | Coastal Processes | Beaches, Oceans | Coastal Processes | Coral Reefs, Oceans | Marine Biology | Marine Habitat, Rare
Organization: Australian Ocean Data Network
XRD analsyis of surface sediment samples collected from the reef rim physiographic zone of Wistari Reef

Wistari Reef is a lagoonal platform reef, situated on the Tropic of Capricorn, within the Capricorn and Bunker region of the southern Great Barrier Reef. Two sediment surface samples were taken from the lagoon area for X-Ray Diffraction Analysis. This was used to compare the relative percentages of aragonite and calcite in the sample. The proportion of aragonite in each sample varies considerably with it representing 73% on the leeward reef edge, and only 39% on the windward reef margin.

Tags: Oceans | Coastal Processes | Coral Reefs, Oceans | Marine Sediments | Carbonate Sediments, amount_of_aragonite, amount_of_calcite
Organization: Australian Ocean Data Network
WAMSI Node 4.4.2-1 - Stock structure of West Coast demersal indicator species - Drift current trajectories from GPS-tracked buoys

The Western Australian Department of Fisheries has been monitoring the trajectories of a series of drifting buoy releases along the Western Australian continental shelf since 2008. The objective of the programme is to study the current system on the continental shelf in relation to the migration of fish and invertebrate larvae, particularly over the summer months when some key pelagic species are spawning and also when the early-stage larvae of the western rock lobster are being transported offshore. To date, most of the releases have been along the lower west coast.

Tags: Oceans | Marine Biology | Fish, Oceans | Ocean Circulation | Buoy Position, Oceans | Ocean Circulation | Ocean Currents, Oceans | Ocean Temperature | Water Temperature, asset_name, battery_voltage, date, julian_hour, julian_hour_last_GPS_fix, latitude, longitude, mode, modem_id, sea_surface_temperature, short_burst_data_time, strain_range_on_drouge, time
Organization: Australian Ocean Data Network
Survey and Assessment of Priority Flora at Mauds Landing

Survey and Assessment of Priority Flora at Mauds Landing. To verify the location and estimate population size of two taxa within the original study area, determine the extent of their distribution beyond original study boundaries and comment on the extent of population losses within the proposed development. A survey and assessment on the local and regional distribution of two Priority flora taxa.

Tags: Biosphere | Vegetation | Vegetation Species, Distribution, Field Surveys | Biological Surveys, Flora
Organization: Australian Ocean Data Network
Zooxanthellate scleractinian corals of the Calamianes Islands, Palawan Province, Philippines (Marine RAP Survey)

Zooxanthellate scleractinian corals were identified at 38 sites in the Calamianes Islands, Palawan Province, Philippines in 1998, using rapid assessment methods. Sites surveyed covered a diverse range of habitats including sandy areas, walls, overhangs, slopes and shallow reef areas. Areas where few or no corals were expected to be found, such as sea grass beds and mangroves were not surveyed. Surveys were conducted using SCUBA to a maximum depth of 40m. The survey method consisted of direct underwater observation of corals, usually during a single 60-90 minute dive at each site. Corals were recorded on a slow ascent from the base of the reef, along a zigzag path to the shallowest part of the reef. New, rare or unusual species were photographed and collected for further study.
 The aims of this survey were:1. to compile an inventory of corals on the reefs of the Calamianes Islands, Palawan Province, Philippines2. to use this information to compare the faunal richness of these islands with other parts of Southeast Asia and adjoining regions.

Organization: Australian Ocean Data Network
SAIMOS - Biological and Flow Cytometry data collected from CTD stations in South Australia, in March 2008

Flow cytometry data was collected in March 2008, 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
2016 SoE Marine Chapter - State and Trends - Sharks and rays (elasmobranchs)

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of quality of species and groups – sharks and rays (elasmobranchs)". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record.

DESCRIPTION OF TAXONOMIC GROUP FOR EXPERT ASSESSMENT
Conservation of elasmobranchs is an increasing priority as evidence of overexploitation of some species becomes increasingly apparent (e.g., Stevens et al. 2000, Graham et al. 2001, Clarke et al. 2006, Dulvy et al. 2008, Dulvy et al. 2014). Australia has ~307 elasmobranch species that occur in marine environments in all bioregions, with about half being endemic.
DATA STREAM(S) USED IN EXPERT ASSESSMENT
Data primarily collected from an expert panel of elasmobranch researchers and fisheries scientists during an IUCN Shark Specialist Group Red List workshop in February 2015 (report still in prep) as part of a FRDC Shark Report Card project (www.sharkreportcard.org)

2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details]
• 2016 •
Assessment grade: Good
Assessment trend: Unclear
Confidence grade: Limited evidence or limited consensus
Confidence trend: Limited evidence or limited consensus
Comparability: Grade and trend are somewhat comparable to the 2011 assessment
• 2011 •
Assessment grade: Good
Assessment trend: Stable
Confidence grade: Limited evidence or limited consensus
Confidence trend: Limited evidence or limited consensus

CHANGES SINCE 2011 SOE ASSESSMENT
Largely agrees with 2011 SOE assessment, however there are few data available on population abundances or trends for most species so trend can only be regarded as unclear rather than stable.

Tags: elasmobranch, expert assessment, population status, rays, sharks
Organization: Australian Ocean Data Network
Sediment distribution patterns in a back-reef lagoon, Ningaloo reef, Western Australia

To examine variation in sediment composition in the back-reef lagoon of Ningaloo Reef, and deduce factors controlling the distribution patterns. This will be done by: determination of the biogenic composition of sediment from different areas of the lagoon; determination of the chemical composition and mineralogy of the biogenic sediment, including use of trace elements as environmental indicators; charting of spatial distribution patterns of the biological, mineralogical and chemical data; testing models for environmental habitat mapping.

Organization: Australian Ocean Data Network
Population genetics of the fissiparous holothurians, Stichopus chloronotus and Holothuria atra, Torres Strait and La Reunion

About 50 individuals from each of 5 populations of the fissiparous holothurian species Stichopus chloronotus and 4 populations of Holothuria atra were collected from the Torres Strait and La Reunion in 1999 to compare patterns of asexual reproduction and to investigate connectivity between widely separated geographic regions.Polymorphic enzyme loci were surveyed using allozyme electrophoresis: PGM, GPI, HK, LP, PGD, PGM, VL in Holothuria atra; and HK, MPI, PGM, TPI, VL in Stichopus chloronotus.The proportions of asexual contributions was assessed from sexually produced individuals.UPMGA cluster analysis using Rogers' genetic distance was carried out.
 The aim of the study was to compare the importance of asexual reproduction between the two regions and between the two species, and to investigate connectivity between holothurian populations in the two oceans.
 Reef locations: Cumberland Reef no.3, Derder and Warrior Reefs in the Torres Strait; and Etang Sale, Planch Alizes, St. Leu and Trou d¿eau at La Reunion.

Organization: Australian Ocean Data Network
CSIRO-Mk3-6-0 model output prepared for CMIP5 rcp60

rcp60 is an experiment of the CMIP5 - Coupled Model Intercomparison Project Phase 5
(http://cmip-pcmdi.llnl.gov/cmip5/). CMIP5 is meant to provide a framework for coordinated
climate change experiments for the next five years and thus includes simulations for
assessment in the AR5 as well as others that extend beyond the AR5.
4.4 rcp60 (4.4 RCP6) - Version 1: Future projection (2006-2100) forced by RCP6. RCP6 is a representative concentration pathway which approximately results in a radiative forcing of 6 W m-2 at year 2100, relative to pre-industrial conditions.
Experiment design: http://cmip-pcmdi.llnl.gov/cmip5/docs/Taylor_CMIP5_design.pdf
List of output variables: http://cmip-pcmdi.llnl.gov/cmip5/docs/standard_output.pdf
Output: time series per variable in model grid spatial resolution in netCDF format
Earth System model and the simulation information: CIM repository
Entry name/title of data are specified according to the Data Reference Syntax
(http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf)
as activity/product/institute/model/experiment/frequency/modeling realm/MIP table/ensemble
member/version number/variable name/CMOR filename.nc.

Tags: 0399 - Other Chemical Sciences, 0401 - Atmospheric Sciences, 0405 - Oceanography, 0406 - Physical Geography and Environmental Geoscience, Atmospheric Sciences, National Computational Infrastructure (NCI), Oceanography, Other Chemical Sciences (Environmental Chemistry), Physical Geography and Environmental Geoscience
Organization: Australian Ocean Data Network
SAIMOS - Biological and Flow Cytometry data collected from CTD stations in South Australia, in March 2017

Flow cytometry data was collected in March 2017, 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