AndreaBozzo/ceres-open-data-index huggingface dataset:
Soil conditions in damaged mangrove forests in north Queensland

In October and November 1991, soil was sampled and the abundance of crabs estimated in nine mangrove forests, located between Bailey's Creek, Cow Bay (north of Port Douglas) and Chunda Bay (south of Townsville). Three forests were chosen in each of following categories:Severely Damaged (mangrove trees removed, soils subjected to earth-works and either erosion or the dumping of spoil) - Spoil Dump, Port Douglas; Marina, Port Douglas; Oyster Point, CardwellDamaged (mangrove trees removed but soils relatively undisturbed) - Bailey's Creek, Cow Bay; Wharf area, Dungeness; Chunda Bay, Cape FergusonControls (mangroves without any obvious physical damage) - Barron Creek, Cairns; Meunga Creek, Cardwell; Coral Creek, Hinchinbrook IslandEach forest was located within 1km of the sea and was, or had been, low-shore, mixed Rhizophora apiculata, Rhizophora stylosa, Bruguiera gymnorhiza and Ceriops tagal forests. The damaged forests had been impacted within the previous 5 years. Within each forest, three randomly selected sites were chosen for sampling during low tide.Relative soil compaction was measured by releasing a metal dropstick (329x6mm, weighing 78.5g) within a 2.0m pipe (16mm diameter) and recording the stick's penetration in the mud. Twenty measurements were made at each site.The relative abundance of crabs was compared by counting the number of crab holes in 5 replicate 1m² quadrats placed randomly at each site.Replicate surface and subsurface (10cm deep) cores were collected at each site and frozen for analysis in the laboratory. The pH of cores was measured using an Orion SA520 pH meter with combination electrode. Grain size analysis was carried out by using a combination of wet sieving and a column settling technique.Soil samples for element analyses were homogenized using an agate Wiley Mill after being dried for 3 days at 80°C. The percentage of total carbon and nitrogen (by weight) was obtained for subsamples of homogenized sediment using a Leco Model 600 CHN Analyser. Another subsample was analysed for percent (by volume) of total phosphorous, potassium, sulfur and iron using a Varian Liberty 200 ICP-Emission Spectrometer (ICP-OES), following a perchloric-nitric acid digestion procedure.
 This research was undertaken to compare chemical, physical and biological characteristics of soils in damaged and undamaged mangrove forests to determine the extent to which soils should be considered when undertaking reconstruction of mangroves.

Organization: Australian Ocean Data Network
Bottlenose Dolphins (Tursiops sp.) in the Swan Estuary

The GPS locations of Bottlenose dolphins in the Swan River Estuary were recorded from October 2001 to June 2003 with the following fields: behaviour, date/time, location, nearest landmark, id's present, depth, feeding activity and the presence of tail slapping and boat begging.

Tags: 41 116019, 41 116020, Oceans | Marine Biology | Marine Mammals, Tursiops aduncus, Tursiops truncatus, human interaction, provisioning
Organization: Australian Ocean Data Network
Short-term movement and dispersal patterns of barramundi in a seasonally closed freshwater habitat in the Northern Territory

Barramundi (Lates calcarifer) were captured by rod and reel angling using lures at Mission Billabong, a freshwater body within the Daly River catchment, southwest of Darwin, Northern Territory. The total length of each captured fish was measured and individuals were fitted with an external dart tag for identification purposes and also a radio transmitter tuned to a unique frequency. Individuals were released into the billabong and re-located once per day, when possible, with a 2MHz receiver. The movements of 29 fish were monitored in the wet (warm) season from 4 to 24 November 2002 and a further 31 fish were monitored in the dry (cool) season from 22nd July to 9 August 2003. When an individual was located, the transmitter number and GPS position was recorded. The distance between consecutive re-locations of individuals was calculated to define the extent of movements of individuals.
 Short term movements patterns of barramundi (Lates calcarifer) were monitored in a seasonally closed freshwater system to determine whether movement and dispersal differed by individual or season.

Organization: Australian Ocean Data Network
AIMS Service or Tool - Real Time and Historic Voyage Track Visualisation and Data Download

This interactive online tool provides access to the voyage information for the AIMS research vessels. Vessel tracks are available for each research trip as are basic description of voyage activities. Vessel positions are updated every 20 minutes and previous voyages are available.
As per the Operates On UUID Reference
AIMS Voyage Tracker Dataset has been updated on 18-11-2021 as a new tool was deployed. See https://doi.org/10.25845/jxdr-7288 AIMS Voyage Tracker Dataset for updated information.

Organization: Australian Ocean Data Network
SAIMOS - Biological and Flow Cytometry data collected from CTD stations in South Australia, in November 2016

Flow cytometry data was collected in November 2016, 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
Geographic distribution of zooxanthella types in 3 coral species, Great Barrier Reef

One small piece of each of 136 colonies of Stylophora pistillata, 116 colonies of Acropora millepora and 121 colonies of Acropora tenuis was collected from 17 sites along a latitudinal and cross-shelf gradient in the central and southern sections of the Great Barrier Reef between 25 June and 1 August 2002.An unrooted Bayesian phylogeny was created of clade C zooxanthellae in the study, based on rDNA ITS1 sequences. Zooxanthellae clades: C1, C2, C3, Cn (one unnamed C subclade), Cmix (more than one C strain harbored simultaneously), D, A (rare in Indo-Pacific corals).Status of coral colonies after the 2002 bleaching event was recorded as: no signs of bleaching, pale/blotched, white, partially dead.Three measures of thermal environment were applied to each site: Maximum three day temperature from satellite SST maps; Cumulative heat index (number of days that satellite SST was &gt;1 standard deviation above average; Index of historical heat stress at the site represented by first principal component for summer maximum satellite SSTs for 1990 to 2000. Note that higher scores are hotter. Collection sites: Allonby Island, Brampton Island, Charity Reef, Chicken Reef, Credlin Reef, Darley Reef, Daydream Island, Dingo Reef, Girder Reef, Keswick Island, Miall Island, Mumford Island, North Keppel Island, Paul Reef, Stone Island, UN19-165, UN21-056.
 To gain an understanding of the geographic distribution of zooxanthella types in 3 coral species along a latitudinal and cross-shelf gradient of the Great Barrier Reef shortly after a major bleaching event.

Organization: Australian Ocean Data Network
Marine Ecological Survey of Bateman Bay, Ningaloo Reef - Oceanwise

In 2002, Oceanwise Environmental scientists initiated a baseline marine ecological survey of Bateman Bay, Ningaloo Reef. 
Research was conducted in collaboration with Murdoch University. A variety of methods were used including manta tow surveys, video transects and baited videos, random spot dives, intensive transects and incidental sightings or observations. Data were collected on the physical environment, macroalgae, seagrass, plankton, coral, molluscs, fish, the intertidal zone, turtles and marine mammals.
Report can be downloaded from this metadata record

Tags: Oceans | Marine Biology | Fish, Oceans | Marine Biology | Marine Invertebrates, Oceans | Marine Biology | Marine Mammals, Oceans | Marine Biology | Marine Microbiota, Oceans | Marine Biology | Marine Reptiles
Organization: Australian Ocean Data Network
Ecological assessment of the Scott Reef system using environmental DNA metabarcoding (WEL)

In October 2021, a total of 94 seawater samples were collected approximately 1m below the surface from the Scott reef system (Figure 1). Samples were collected at 10 sites spread across the three atolls (South Scott, North Scott, and Seringapatam). At each site, a minimum of five replicate 1L samples were collected in sterile Nalgene bottles sites by snorkellers. We also included for comparison seawater samples collected from the Rowley Shoals (n=13), a neighbouring oceanic atoll system with pristine coral reef communities, and from inside the Darwin Harbour (n=6), a tidally-dominated turbid inshore environment. Samples inside Darwin Harbour were collected using the RV Solander&rsquo;s Niskin array. Water samples were stored on ice until filtration within 6 hours of sample collection.
A series of control samples that consisted of the 10-20% bleach solution used to rinse collection bottles were also collected. All samples were filtered using a 250 mL funnel EZ-Fit filtration unit with 0.48 &mu;m mixed cellulose ester membranes and an EZ-Fit Manifold base (3-place) from Merck Millipore (Merck Group, Burlington, USA). Gloves were changed and the manifold base and cup were sterilized with a 10% bleach solution between the filtering of samples from different sites. Following filtration, the filter papers were rolled and kept in cryogenic tubes at -20&deg;C until transport and storage at -80&deg;C.

Organization: Australian Ocean Data Network
Pre-emergent phytotoxicity using image analysis

A simple quantitative bioassay was developed using widely available technology to determine pre-emergent phytotoxicity. Digitaria didactyla (Queensland Blue Couch Grass) was assessed by analysing digital images of the plants growing in microtitre plates for the effects of herbicides on germination. The herbicides tested were metsulfuron, triasulfuron, fluometuron atrazine, simazine and prometryn. Images of each 24-well microtitre plate (taken with a digital camera 7-10 days after planting), were analysed using a public domain image processing program, and a filter (developed using plugins available within the program) selected pixels within the green spectrum. Pixel counting took place using a spreadsheet function.
 To investigate the use of microtitre plates for the discovery of phytotoxic compounds within higher plants.
 This bioassay system allows rapid throughput of test samples with minimum handling.

Organization: Australian Ocean Data Network
IMOS - Ocean Gliders - Slocum glider deployment in New South Wales off Port Stephens (November - December 2008)

The dataset contains temperature, salinity and biological parameters like for example dissolved oxygen and turbidity data measured by a Slocum glider in the region of Port Stephens (New South Wales).
The Ocean Gliders Facility (formerly known as the Australian National Facility for Ocean Gliders (ANFOG)), manages Slocum gliders to be deployed on the continental shelf.
The variables available in this dataset are:
Temperature, salinity, conductivity, density, pressure, chromophoric dissolved oxygen matter, dissolved oxygen, fluorescence and backscatter coefficient at 660nm.

Tags: CTD (Conductivity-Temperature-Depth Profilers), Coloured Dissolved Organic Matter (CDOM), Countries | Australia, Fluorometers, Glider, IMOS Node | Bluewater and Climate, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Chemistry | Oxygen, Oceans | Ocean Chemistry | Suspended Solids, Oceans | Ocean Circulation | Ocean Currents, Oceans | Ocean Optics | Fluorescence, Oceans | Ocean Optics | Turbidity, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Conductivity, Slocum Glider, States, Territories (Australia) | New South Wales, concentration_of_coloured_dissolved_organic_matter, fluorescence_in_sea_water, mass_concentration_of_oxygen_in_sea_water, sea_water_electrical_conductivity, sea_water_pressure, sea_water_salinity, sea_water_temperature, volumetric_backscatter_coefficient
Organization: Australian Ocean Data Network
Chemical and biological assessment of produced formation water (PFW) at Harriet A platform on the North West Shelf, Western Australia

A comprehensive biological and chemical assessment of the fate, effects and potential risks associated with Produced Formation Water (PFW) were conducted at the Harriet A platform on the North West Shelf of Australia. A controlled in situ caging study was conducted using a Australian, tropical reef species, Stripey seaperch (Lutjanus carponotatus), deployed in 6 separate galvanised steel cages set 1m subsurface at 3 stations; Site A (near-field~ 300 m), Site B (far-field, ~ 1000 m) and Site C, a reference site. Samples were collected at T= 0, T= 3 and T=10 days for EROD, cytochrome P450, bile metabolites, CYP1A, CYP2K1- and CYP2M1-like proteins, vitellogenin, GST, HSI, and histopathological assessment of liver and gills. In addition, time-integrated water column samplers (SPMDs) were deployed at all 3 sites to assess in situ petroleum hydrocarbon concentrations. The results from a 3 factor nested ANOVA, demonstrated that were no effects of cages nested in site, and no interactions between cages and time of sampling, therefore the effect of cages was removed from all subsequent analyses. As a result of univariate analysis (ANOVA), bile metabolites, CYP1A, CYP2M1- and CYP2K1-like proteins, and histopathological assessment of livers and gills were statistically significant (p &lt; 0.05) at Site A after 10 days of exposure to PFW, corresponding with higher levels of PAHs at this site. Analysis by Principal Component established trends that the CYP-like proteins explained most of the variation amongst all biomarker responses, and these correlations were driven largely by the effects of site (Site A) and time of sampling (T=10). This study demonstrated that PFW discharged into this shallow tropical ecosystem is causing environmental degradation of water quality within close proximity to the Harriet A platform (~ 300 m).
 to assess the fate, effects and potential risks associated with Produced Formation Water (PFW) at the Harriet A platform on the North West Shelf of Australia.
 A separate metadata record covers a pilot study for PFW.

Organization: Australian Ocean Data Network
Chemical microenvironment within complex multispecies macroalgae assemblages

-- Layton et al. Chemical microenvironments within macroalgal assemblages: implications for the inhibition of kelp recruitment by turf algae. Limnology &amp; Oceanography. DOI:10.1002/lno.11138 -- 
Kelp forests around the world are under increasing pressure from anthropogenic stressors. A widespread consequence is that in many places, complex and highly productive kelp habitats have been replaced by structurally simple and less productive turf algae habitats. Turf algae habitats resist re-establishment of kelp via recruitment inhibition; however little is known about the specific mechanisms involved. One potential factor is the chemical environment within the turf algae and into which kelp propagules settle and develop. Using laboratory trials, we illustrate that the chemical microenvironment (O2 concentration and pH) 0.0–50 mm above the benthos within four multispecies macroalgal assemblages (including a turf-sediment assemblage and an Ecklonia radiata kelp-dominated assemblage) are characterised by elevated O2 and pH relative to the surrounding seawater. Notably however, O2 and pH were significantly higher within turf-sediment assemblages than in kelp-dominated assemblages, and at levels that have previously been demonstrated to impair the photosynthetic or physiological capacity of kelp propagules. Field observations of the experimental assemblages confirmed that recruitment of kelp was significantly lower into treatments with dense turf algae than in the kelp-dominated assemblages. We demonstrate differences between the chemical microenvironments of kelp and turf algae assemblages that correlate with differences in kelp recruitment, highlighting how degradation of kelp habitats might result in the persistence of turf algae habitats and the localised absence of kelp.

Tags: Recruitment of Stage 1 juvenile kelp per paver, Temperate Reef, depth of turf-sediment matrix, macroalgae biomass by species name, water flow within flume
Organization: Australian Ocean Data Network
Suspension feeders and energy flow through reefs

Suspension feeders - animals that capture food particles from the water - exert a major influence on the aquatic environment, and most groups of animals, from vertebrates to protozoa, have some members for whom suspension feeding is their major means of obtaining nutrients. 
Due to their impact on plankton populations and suspended organic materials suspension feeders influence food availability and energy transfer in most marine and freshwater habitats. Many suspension feeders, such as bivalve molluscs, sponges and corals, are of importance commercially, in terms of aquaculture, exploitation of wild stocks, and, increasingly, tourism for coral reef ecosystems.
An understanding of the implications of environmental change for optimal habitat ranges, growth rates and potential future exploitation of suspension-feeding organisms requires the ability to predict responses of these organisms to changes in physical factors such as water flow, temperature and particle loads.
Research projects in this area include:
Flow-mediated responses to environmental change
Viscosity effects on ciliary feeding
Heterotrophy in reef-building corals
Energy flow across coral reefs

Tags: Biomechanics, Energy Flow, Filter Feeders, Fluid Dynamics, Oceans | Coastal Processes | Coral Reefs, Particle Capture, Suspension Feeders
Organization: Australian Ocean Data Network
IMOS - Autonomous Underwater Vehicles - SIRIUS CAMPAIGN: WESTERN AUSTRALIA, APRIL 2011

Rottnest Island, Jurien Bay and the Abrolhos (Kendrick, Smale): AUV benthic reference sites were established at Rottnest Island, Jurien Bay and the Abrolhos Islands. Large swell at some sites meant that the vehicle was being moved around a lot leading to some patchy holes in the meshes, predominantly at the Rottnest site.  The  information available to help plan dive locations became less detailed as the deployments moved further north.  The dives at the Abrolhos were planned using simple nautical charts and featured more sand and coral than kelp. It would be useful to secure multibeam surveys in the region to help plan future dives

Tags: AUV | Autonomous Underwater Vehicle, CTD (Conductivity-Temperature-Depth Profilers), Cameras | Still Cameras - underwater, Coloured Dissolved Organic Matter (CDOM), Countries | Australia, Current Meters/Profilers | Acoustic Doppler Current Profiler (ADCP), Data Loggers, Digital Imaging (acquisition and/or analysis), Field Surveys | Underwater Surveys, Fluorometers, Marine Planning Regions (Australia) | South-east, Oceans | Bathymetry | Seafloor Topography, Oceans | Bathymetry | Water Depth, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Chemistry | Organic Matter, Oceans | Ocean Chemistry | Oxygen, Oceans | Ocean Optics | Fluorescence, Oceans | Ocean Optics | Turbidity, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Conductivity, SONAR, Seabed Vehicles, States, Territories (Australia) | Tasmania, Turbulence Sensors, altitude, concentration_of_coloured_dissolved_organic_matter, depth, heading, latitude, longitude, mass_concentration_of_chlorophyll_in_sea_water, optical_backscatter, platform_pitch_angle, platform_roll_angle, sea_water_salinity, sea_water_temperature
Organization: Australian Ocean Data Network